Re: [gmx-users] help about ibi
Hi, Something went wrong earlier in your workflow. Check your log files, etc. Mark On Nov 13, 2013 3:57 AM, guozhicheng222 guozhicheng...@126.com wrote: Hi: When I am running the ibi procedure, I get the following error message: A coordinate in file conf.gro does not contain a '.' Additionally, I check the coordinate file of confout.gro in step_001. It showed that 'nan' symbol appeared in confout.gro. What is wrong with this? How can I fix it? I am very appreciating for anyone's help. Best Wishes! Zhicheng Guo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Recompile Gromacs 4.6.3
For just modifying a file, just doing make is sufficient. I would recommend not installing the modified version (since you can run the build/src/kernel/mdrun directly), or if you must install, to use the suffixing options available in the ccmake advanced mode. Mark On Nov 13, 2013 2:48 PM, Jheng Wei Li lijheng...@gmail.com wrote: Hello, all I intend to make some modification on minimize.c in mdlib. Do I need to do cmake make make install all over again? Or is there a quick way for recompiling? Thanks for any tips. JhengWei Li Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] error while running pdb2gmx
Probably the default behaviour of pdb2gmx for termini is not appropriate for your input. Use pdb2gmx -ter and choose wisely Mark On Nov 13, 2013 12:03 PM, hasthi durgs7kr...@gmail.com wrote: Hello GROMACS users, I have phosphorylated Serine residue in my protein (140 residues) of interest, now when I run pdb2gmx I get this following error Atom OXT in residue ALA 140 was not found in rtp entry ALA with 6 atoms while sorting atoms. I checked aminoacid.rtp, there is no separate entry for OXT there.When I did the simulation for the same protein prior phosphorylation I did not get this error. What is the reason for this and how should I rectify this error? Please help me with this regard Regards, Hasthi -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] GROMACS 4.6.4 is released
Hi GROMACS users, GROMACS 4.6.4 is officially released. It contains numerous bug fixes, and some noteworthy simulation performance enhancements (particularly with GPUs!). We encourage all users to upgrade their installations from earlier 4.6-era releases. You can find the code, manual, release notes, installation instructions and test suite at the links below. Note that some tests have been added, and the manual has changed only in chapter 7 and appendix D. ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.6.4.tar.gz ftp://ftp.gromacs.org/pub/manual/manual-4.6.4.pdf http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x#Release_notes_for_4.6.4 http://www.gromacs.org/Documentation/Installation_Instructions http://gromacs.googlecode.com/files/regressiontests-4.6.4.tar.gz Happy simulating! The GROMACS team -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] About Compiler Compatibility for Gromacs 4.6.2 Compilation
On Nov 10, 2013 10:04 AM, Mark Abraham mark.j.abra...@gmail.com wrote: Yes (unless you are using AMD cpus), per the installation instructions, although you will probably do slightly better with GCC 4.7, and should not do a new install of 4.6.2 after 4.6.3 is released. In particular, 4.6.2 has an affinity-related performance regression when using external MPI libraries. Mark On Nov 10, 2013 7:55 AM, vidhya sankar scvsankar_...@yahoo.com wrote: Dear Justin and Mark Thank you for your Previous reply Can i Use the Following Intel Compiler for grmacs 4.6.2 in centos Linux OS ? Intel® C++ Composer XE 2013 for Linux it Includes Intel® C++ Compiler, Intel® Integrated Performance Primitives 7.1, Intel® Math Kernel Library 11.0, Intel Cilk™ Plus, the Intel® Threading Building Blocks (Intel® TBB)” -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: mdrun on 8-core AMD + GTX TITAN (was: Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs)
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman mpi...@gmail.com wrote: Hi Szilard, Thank you very much for your suggestions. Actually, I was jumping to conclusions too early, as you mentioned AMD cluster, I assumed you must have 12-16-core Opteron CPUs. If you have an 8-core (desktop?) AMD CPU, than you may not need to run more than one rank per GPU. Yes, we do have independent clusters of AMD, AMD opteron, Intel Corei7. All nodes of three clusters are installed with (at least) 1 GPU card. I have run the same test on these three clusters. Let's focus on a basic scaling issue: One GPU v.s Two GPUs within the same node of 8-core AMD cpu. Using 1 GPU, we can have a performance of ~32 ns/day. Using two GPU, we gain not much more ( ~38.5 ns/day ). It is about ~20% more performance. However, this is not really true because in some tests, I also saw only 2-5% more, which really surprised me. Neither run had a PP-PME work distribution suitable for the hardware it was running on (and fixing that for each run requires opposite changes). Adding a GPU and hoping to see scaling requires that there be proportionately more GPU work available to do, *and* enough absolute work to do. mdrun tries to do this, and reports early in the log file, which is one of the reasons Szilard asked to see whole log files - please use a file sharing service to do that. As you can see, this test was made on the same node regardless of networking. Can the performance be improved say 50% more when 2 GPUs are used on a general task ? If yes, how ? Indeed, as Richard pointed out, I was asking for *full* logs, these summaries can't tell much, the table above the summary entitled R E A L C Y C L E A N D T I M E A C C O U N T I N G as well as other reported information across the log file is what I need to make an assessment of your simulations' performance. Please see below. However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. After I test all three clusters, I found it may NOT be an issue of AMD cpus. Intel cpus has the SAME scaling issue. However, I am curious as to how you justify the setup of 2-4 ranks sharing GPUs ? Can you please explain it a bit more ? NUMA effects on multi-socket AMD processors are particularly severe; the way GROMACS uses OpenMP is not well suited to them. Using a rank (or two) per socket will greatly reduce those effects, but introduces different algorithmic overhead from the need to do DD and explicitly communicate between ranks. (You can see the latter in your .log file snippets below.) Also, that means the parcel of PP work available from a rank to give to the GPU is smaller, which is the opposite of what you'd like for GPU performance and/or scaling. We are working on a general solution for this and lots of related issues in the post-5.0 space, but there is a very hard limitation imposed by the need to amortize the cost of CPU-GPU transfer by having lots of PP work available to do. You could try running mpirun -np 4 mdrun -ntomp 2 -gpu_id 0011 but I suspect this won't help because your scaling issue Your guess is correct but why is that ? it is worse. The more nodes are involved in a task, the performance is worse. in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). What dose it mean let alone with PME ? how to do so ? by mdrun ? I do know mdrun -npme to specify PME process. If using PME (rather than RF), network demands are more severe. Thank you. Dwey ### One GPU R E A L C Y C L E A N D T I M E A C C O U N T I N G Computing: Nodes Th. Count Wall t (s) G-Cycles % - Neighbor search18 11 431.81713863.390 1.6 Launch GPU ops.18501 472.90615182.556 1.7 Force 185011328.61142654.785 4.9 PME mesh 18501 11561.327 371174.09042.8 Wait GPU local 185016888.008 221138.11125.5 NB X/F buffer ops. 189911216.49939055.455 4.5 Write traj.18 1030 12.741 409.039 0.0 Update 185011696.35854461.226 6.3 Constraints185011969.72663237.647 7.3 Rest 11458.82046835.133 5.4 - Total 1 27036.812 868011.431 100.0
Re: [gmx-users] problem in running mdrun command
Hi, There's nothing GROMACS-specific here - something about your MPI installation, configuration or use is pretty wrong, but we can't help work out what. Mark On Sun, Nov 10, 2013 at 12:31 PM, S.Chandra Shekar chandrashe...@iisertvm.ac.in wrote: Dear all I encounter a problem while running command mdrun_mpi -v -deffnm em in gromacs. I am new to the gromacs. i just ran test calculation, *simulation of lyzozyme in water*. i am able to generate gro, tpr files. But in the final step i got following error. Thanks in advance. [localhost.localdomain:23122] mca: base: component_find: paffinity mca_paffinity_linux uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: paffinity mca_paffinity_linux uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_dash_host uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_gridengine uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: ras mca_ras_localhost uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_hnp uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_orted uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: errmgr mca_errmgr_proxy uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: iof mca_iof_proxy uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23123] mca: base: component_find: iof mca_iof_svc uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost.localdomain:23122] mca: base: component_find: rcache mca_rcache_rb uses an MCA interface that is not recognized (component MCA v1.0.0 != supported MCA v2.0.0) -- ignored [localhost:23122] *** Process received signal *** [localhost:23122] Signal: Segmentation fault (11) [localhost:23122] Signal code: Address not mapped (1) [localhost:23122] Failing at address: 0x4498 [localhost:23122] [ 0] /lib64/libpthread.so.0() [0x3fcee0f500] [localhost:23122] [ 1] /usr/local/lib/libmpi.so.1(PMPI_Comm_size+0x4e) [0x2acc6d93727e] [localhost:23122] [ 2] /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(gmx_setup+0x32) [0x2acc6d195e02] [localhost:23122] [ 3] /usr/local/gromacs/bin/../lib/libgmx_mpi.so.8(init_par+0x51) [0x2acc6d234251] [localhost:23122] [ 4] mdrun_mpi(cmain+0x11f9) [0x435799] [localhost:23122] [ 5] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3fcea1ecdd] [localhost:23122] [ 6] mdrun_mpi() [0x406ee9] [localhost:23122] *** End of error message *** Segmentation fault (core dumped) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Reproducing results with independent runs
On Sat, Nov 9, 2013 at 9:36 AM, alex.bjorling alex.bjorl...@gmail.comwrote: Dear users, I am investigating protein crystal packing artifacts by doing equilibrium simulations starting from a crystal structure. I would like to know if the relaxations i see are reproducible, in the sense that many simulations with independent velocities give the same general result. My plans is to do only one set of (first NVT then NPT) equilibrations with position restraints. Then, I thought I'd do a shorter NPT run with position restraints, with more frequent output and using the trr snapshots as starting points for production runs. The only question then is how far apart these snapshots need to be to guarantee independent velocities. Attached is the velocity autocorrelation for the Protein group. It seems to me that using snapshots 1ps apart would do it, since the autocorrelation has decayed by then. Is this a valid approach? That the observations are uncorrelated (because the autocorrelation time has elapsed) does not imply that trajectories started from successive snapshots would be independent - in the absence of floating-point or load-balancing artefacts leading to numerical divergence, the separate simulations would nearly reproduce each other! Since you have to wait for a period of divergence anyway, you might as well generate new velocities after an initial stage of equilibration, equilibrate further, and have no independence question to answer. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5
Hi, That shouldn't happen if your MPI library is working (have you tested it with other programs?) and configured properly. It's possible this is a known bug, so please let us know if you can reproduce it in the latest releases. Mark On Fri, Nov 8, 2013 at 6:55 AM, Qin Qiao qiaoqi...@gmail.com wrote: Dear all, I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT ensemble, and I got the following errors when I tried to use 2 cores per replica: [node-ib-4.local:mpi_rank_25][error_sighandler] Caught error: Segmentation fault (signal 11) [node-ib-13.local:mpi_rank_63][error_sighandler] Caught error: Segmentation fault (signal 11) ... Surprisingly, it worked fine when I tried to use only 1 core per replica.. I have no idea what caused the problem.. Could you give me some advice? ps. the command I used is srun .../gromacs-4.5.5-mpi-slurm/bin/mdrun_infiniband -s remd_.tpr -multi 48 -replex 1000 -deffnm remd_ -cpi remd_.cpt -append Best Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne...@gmail.comwrote: Really? Of course. With openmp gets to use all your cores for PME+bondeds+stuff while the GPU does PP. Any version without openmp gets to use one core per domain, which is bad. An what about gcc+mpi? should I expect any improvement? Run how and compared with what? Using an external MPI library within a single node is a complete waste of time compared with the alternatives (thread-MPI, OpenMP, or both). Mark On Thu, Nov 7, 2013 at 6:51 PM, Mark Abraham mark.j.abra...@gmail.com wrote: You will do much better with gcc+openmp than icc-openmp! Mark On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.com wrote: Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but openmp goes horrobly in our cluster, I don't know why): setenv CC /opt/intel/bin/icc setenv CXX /opt/intel/bin/icpc setenv F77 /opt/intel/bin/ifort setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ mkdir build cd build cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ make make install cd .. rm -rf build On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote: Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http
Re: [gmx-users] mpi segmentation error in continuation of REMD simulation with gromacs 4.5.5
OK, thanks. Please open a new issue at redmine.gromacs.org, describe your observations as above, and upload a tarball of your input files. Mark On Fri, Nov 8, 2013 at 2:14 PM, Qin Qiao qiaoqi...@gmail.com wrote: On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, That shouldn't happen if your MPI library is working (have you tested it with other programs?) and configured properly. It's possible this is a known bug, so please let us know if you can reproduce it in the latest releases. Mark Hi, I installed different versions of gromacs with the same MPI library. Surprisingly, the problem doesn't occur in gromacs-4.5.1.. but still in the gromacs-4.6.3... The MPI version is MVAPICH2-1.9a for infinite band. Best, Qin On Fri, Nov 8, 2013 at 6:55 AM, Qin Qiao qiaoqi...@gmail.com wrote: Dear all, I'm trying to continue a REMD simulation using gromacs4.5.5 under NPT ensemble, and I got the following errors when I tried to use 2 cores per replica: [node-ib-4.local:mpi_rank_25][error_sighandler] Caught error: Segmentation fault (signal 11) [node-ib-13.local:mpi_rank_63][error_sighandler] Caught error: Segmentation fault (signal 11) ... Surprisingly, it worked fine when I tried to use only 1 core per replica.. I have no idea what caused the problem.. Could you give me some advice? ps. the command I used is srun .../gromacs-4.5.5-mpi-slurm/bin/mdrun_infiniband -s remd_.tpr -multi 48 -replex 1000 -deffnm remd_ -cpi remd_.cpt -append Best Qin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs
First, there is no value in ascribing problems to the hardware if the simulation setup is not yet balanced, or not large enough to provide enough atoms and long enough rlist to saturate the GPUs, etc. Look at the log files and see what complaints mdrun makes about things like PME load balance, and the times reported for different components of the simulation, because these must differ between the two runs you report. diff -y -W 160 *log |less is your friend. Some (non-GPU-specific) background information in part 5 here http://www.gromacs.org/Documentation/Tutorials/GROMACS_USA_Workshop_and_Conference_2013/Topology_preparation%2c_%22What's_in_a_log_file%22%2c_basic_performance_improvements%3a_Mark_Abraham%2c_Session_1A (though I recommend the PDF version) Mark On Thu, Nov 7, 2013 at 6:34 AM, James Starlight jmsstarli...@gmail.comwrote: I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave me the same performance mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test, mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test, Doest it be due to the small CPU cores or addition RAM ( this system has 32 gb) is needed ? OR may be some extra options are needed in the config? James 2013/11/6 Richard Broadbent richard.broadben...@imperial.ac.uk Hi Dwey, On 05/11/13 22:00, Dwey Kauffman wrote: Hi Szilard, Thanks for your suggestions. I am indeed aware of this page. In a 8-core AMD with 1GPU, I am very happy about its performance. See below. My intention is to obtain a even better one because we have multiple nodes. ### 8 core AMD with 1 GPU, Force evaluation time GPU/CPU: 4.006 ms/2.578 ms = 1.554 For optimal performance this ratio should be close to 1! NOTE: The GPU has 20% more load than the CPU. This imbalance causes performance loss, consider using a shorter cut-off and a finer PME grid. Core t (s) Wall t (s)(%) Time: 216205.51027036.812 799.7 7h30:36 (ns/day)(hour/ns) Performance: 31.9560.751 ### 8 core AMD with 2 GPUs Core t (s) Wall t (s)(%) Time: 178961.45022398.880 799.0 6h13:18 (ns/day)(hour/ns) Performance: 38.5730.622 Finished mdrun on node 0 Sat Jul 13 09:24:39 2013 I'm almost certain that Szilard meant the lines above this that give the breakdown of where the time is spent in the simulation. Richard However, in your case I suspect that the bottleneck is multi-threaded scaling on the AMD CPUs and you should probably decrease the number of threads per MPI rank and share GPUs between 2-4 ranks. OK but can you give a example of mdrun command ? given a 8 core AMD with 2 GPUs. I will try to run it again. Regarding scaling across nodes, you can't expect much from gigabit ethernet - especially not from the cheaper cards/switches, in my experience even reaction field runs don't scale across nodes with 10G ethernet if you have more than 4-6 ranks per node trying to communicate (let alone with PME). However, on infiniband clusters we have seen scaling to 100 atoms/core (at peak). From your comments, it sounds like a cluster of AMD cpus is difficult to scale across nodes in our current setup. Let's assume we install Infiniband (20 or 40GB/s) in the same system of 16 nodes of 8 core AMD with 1 GPU only. Considering the same AMD system, what is a good way to obtain better performance when we run a task across nodes ? in other words, what dose mudrun_mpi look like ? Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nabble. com/Gromacs-4-6-on-two-Titans-GPUs-tp5012186p5012279.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't
Re: [gmx-users] nose-hoover vs v-rescale in implicit solvent
I think either is correct for practical purposes. Mark On Thu, Nov 7, 2013 at 8:41 AM, Gianluca Interlandi gianl...@u.washington.edu wrote: Does it make more sense to use nose-hoover or v-rescale when running in implicit solvent GBSA? I understand that this might be a matter of opinion. Thanks, Gianluca - Gianluca Interlandi, PhD gianl...@u.washington.edu +1 (206) 685 4435 http://artemide.bioeng.washington.edu/ Research Scientist at the Department of Bioengineering at the University of Washington, Seattle WA U.S.A. - -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: single point calculation with gromacs
On Wed, Nov 6, 2013 at 4:07 PM, fantasticqhl fantastic...@gmail.com wrote: Dear Justin, I am sorry for the late reply. I still can't figure it out. It isn't rocket science - your two .mdp files describe totally different model physics. To compare things, change as few things as necessary to generate the comparison. So use the same input .mdp file for the MD vs EM single-point comparison, just changing the integrator line, and maybe unconstrained-start (I forget the details). And be aware of http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy Mark Could you please send me the mdp file which was used for your single point calculations. I want to do some comparison and then solve the problem. Thanks very much! All the best, Qinghua -- View this message in context: http://gromacs.5086.x6.nabble.com/single-point-calculation-with-gromacs-tp5012084p5012295.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: CHARMM .mdp settings for GPU
Hi, It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the original paper's coulomb settings can be taken with a grain of salt for use with PME - others' success in practice should be a guideline here. The good news is that the default GROMACS PME settings are pretty good for at least some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU auto-tuning of parameters in 4.6 is designed to preserve the right sorts of things. LJ is harder because it would make good sense to preserve the way CHARMM did it, but IIRC you can't use something equivalent to the CHARMM LJ shift with the Verlet kernels, either natively or with a table. We hope to fix that in 5.0, but code is not written yet. I would probably use vdwtype = cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2, but I don't run CHARMM simulations for a living ;-) Mark On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.comwrote: Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote: Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] installing gromacs 4.6.1 with openmpi
Sounds like a non-GROMACS problem. I think you should explore configuring OpenMPI correctly, and show you can run an MPI test program successfully. Mark On Thu, Nov 7, 2013 at 5:51 PM, niloofar niknam niloofae_nik...@yahoo.comwrote: Dear gromacs users I have installed gromacs 4.6.1 with cmake 2.8.12, fftw3.3.3 and openmpi-1.6.4 on a single machine with 8 cores(Red Hat Enterprise linux 6.1) . During openmpi installation ( I used make -jN) and also in gromacs installation ( I used make -j N command), everything seemed ok but when I want to use mpirun -np N mdrun I face this error: mpiexec failed: gethostbyname_ex failed for Bioinf2 (I can run mdrun with just one cpu).Any suggestion would be highly appreciated. thanks in advance, Niloofar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: CHARMM .mdp settings for GPU
Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM switch differs from the GROMACS switch (Justin linked a paper here with the CHARMM switch description a month or so back, but I don't have that link to hand). Mark On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan rajatdesi...@gmail.comwrote: Thank you, Mark. I think that running it on CPUs is a safer choice at present. On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, It's not easy to be explicit. CHARMM wasn't parameterized with PME, so the original paper's coulomb settings can be taken with a grain of salt for use with PME - others' success in practice should be a guideline here. The good news is that the default GROMACS PME settings are pretty good for at least some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the GPU auto-tuning of parameters in 4.6 is designed to preserve the right sorts of things. LJ is harder because it would make good sense to preserve the way CHARMM did it, but IIRC you can't use something equivalent to the CHARMM LJ shift with the Verlet kernels, either natively or with a table. We hope to fix that in 5.0, but code is not written yet. I would probably use vdwtype = cut-off, vdw-modifier = potential-shift-verlet and rcoulomb=rlist=rvdw=1.2, but I don't run CHARMM simulations for a living ;-) Mark On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan rajatdesi...@gmail.com wrote: Dear All, Any suggestions? Thank you. -- View this message in context: http://gromacs.5086.x6.nabble.com/CHARMM-mdp-settings-for-GPU-tp5012267p5012316.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: LIE method with PME
If the long-range component of your electrostatics model is not decomposable by group (which it isn't), then you can't use that with LIE. See the hundreds of past threads on this topic :-) Mark On Thu, Nov 7, 2013 at 8:34 PM, Williams Ernesto Miranda Delgado wmira...@fbio.uh.cu wrote: Hello I performed MD simulations of several Protein-ligand complexes and solvated Ligands using PME for log range electrostatics. I want to calculate the binding free energy using the LIE method, but when using g_energy I only get Coul-SR. How can I deal with Ligand-environment long range electrostatic interaction using gromacs? I have seen other discussion lists but I couldn't arrive to a solution. Could you please help me? Thank you Williams -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
You will do much better with gcc+openmp than icc-openmp! Mark On Thu, Nov 7, 2013 at 9:17 PM, Jones de Andrade johanne...@gmail.comwrote: Did it a few days ago. Not so much of a problem here. But I compiled everything, including fftw, with it. The only error I got was that I should turn off the separable compilation, and that the user must be in the group video. My settings are (yes, I know it should go better with openmp, but openmp goes horrobly in our cluster, I don't know why): setenv CC /opt/intel/bin/icc setenv CXX /opt/intel/bin/icpc setenv F77 /opt/intel/bin/ifort setenv CMAKE_PREFIX_PATH /storage/home/johannes/lib/fftw/vanilla/ mkdir build cd build cmake .. -DGMX_GPU=ON -DCUDA_SEPARABLE_COMPILATION=OFF -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda -DGMX_OPENMP=OFF -DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DMPIEXEC_MAX_NUMPROCS=1024 -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON -DCMAKE_INSTALL_PREFIX=/storage/home/johannes/bin/gromacs/vanilla/ make make install cd .. rm -rf build On Thu, Nov 7, 2013 at 3:02 PM, Mark Abraham mark.j.abra...@gmail.com wrote: icc and CUDA is pretty painful. I'd suggest getting latest gcc. Mark On Thu, Nov 7, 2013 at 2:42 PM, ahmed.sa...@stfc.ac.uk wrote: Hi, I'm having trouble compiling v 4.6.3 with GPU support using CUDA 5.5.22. The configuration runs okay and I have made sure that I have set paths correctly. I'm getting errors: $ make [ 0%] Building NVCC (Device) object src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o icc: command line warning #10006: ignoring unknown option '-dumpspecs' /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/crt1.o: In function `_start': (.text+0x20): undefined reference to `main' CMake Error at cuda_tools_generated_pmalloc_cuda.cu.o.cmake:206 (message): Error generating /apps/src/gromacs/gromacs-4.6.3/src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir//./cuda_tools_generated_pmalloc_cuda.cu.o make[2]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/./cuda_tools_generated_pmalloc_cuda.cu.o] Error 1 make[1]: *** [src/gmxlib/cuda_tools/CMakeFiles/cuda_tools.dir/all] Error 2 make: *** [all] Error 2 Any help would be appreciated. Regards, Ahmed. -- Scanned by iCritical. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: LIE method with PME
I'd at least use RF! Use a cut-off consistent with the force field parameterization. And hope the LIE correlates with reality! Mark On Nov 7, 2013 10:39 PM, Williams Ernesto Miranda Delgado wmira...@fbio.uh.cu wrote: Thank you Mark What do you think about making a rerun on the trajectories generated previously with PME but this time using coulombtype: cut-off? Could you suggest a cut off value? Thanks again Williams -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Number of water molecules around any methyl carbon
Count the number of O observed near each C singly and compare the four numbers. Mark On Nov 6, 2013 4:57 PM, rankinb rank...@purdue.edu wrote: Hi all, I would like to calculate the number of water molecules around any of the methyl carbon atoms of tert-butyl alcohol. Currently, I have defined an index group containing all three of the methyl carbon atoms and used trjorder -nshell to calculate the number of oxygen atoms within a specified cutoff distance of this index group. What I am trying to figure out is whether this method results in the number of oxygen atoms around any single methyl carbon or all methyl carbon atoms. Does anyone have any insights regarding this problem? If the described method does not calculate the number of oxygen atoms around all of the methyl carbon atoms, is there a way to do so, without overcounting? Thanks, Blake PhD Candidate Purdue University Ben-Amotz Lab -- View this message in context: http://gromacs.5086.x6.nabble.com/Number-of-water-molecules-around-any-methyl-carbon-tp5012297.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Analysis tools and triclinic boxes
Hi, They ought to, and we hope they do, but historically quality control of analysis tools was threadbare, there is no testing of that kind of thing now, and certainly no implied warranty. Especially at the existing price point! ;-) That comment could easily refer to (or be) an archaic code version, I'm afraid. If you have doubts, please try to verify with a simple system the behaviour you expect. Mark On Mon, Nov 4, 2013 at 7:29 PM, Stephanie Teich-McGoldrick stephani...@gmail.com wrote: Dear all, I am using gromacs 4.6.3 with a triclinic box. Based on the manual and mail list, it is my understanding that the default box shape in gromacs in a triclinic box. Can I assume that all the analysis tools also work for a triclinic box. Cheers, Stephanie -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] stopped simulation
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Triple counting is not possible, per minimum-image convention. I think Ehsan's report of a 0.5nm box size is probably wrong, e.g. per its documentation, editconf -d 0.5 does not produce a 0.5nm box. Mark Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long
Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
On Tue, Nov 5, 2013 at 12:55 PM, James Starlight jmsstarli...@gmail.comwrote: Dear Richard, 1) mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test gave me performance about 25ns/day for the explicit solved system consisted of 68k atoms (charmm ff. 1.0 cutoofs) gaves slightly worse performation in comparison to the 1) Richard suggested mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test, which looks correct to me. -ntomp 6 is probably superfluous Mark finally 3) mdrun -deffnm md_CaM_test running in the same regime as in the 2) so its also gave me 22ns/day for the same system. How the efficacy of using of dual-GPUs could be increased? James 2013/11/5 Richard Broadbent richard.broadben...@imperial.ac.uk Dear James, On 05/11/13 11:16, James Starlight wrote: My suggestions: 1) During compilstion using -march=corei7-avx-i I have obtained error that somethng now found ( sorry I didnt save log) so I compile gromacs without this flag 2) I have twice as better performance using just 1 gpu by means of mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test than using of both gpus mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v -deffnm md_CaM_test in the last case I have obtained warning WARNING: Oversubscribing the available 12 logical CPU cores with 24 threads. This will cause considerable performance loss! here you are requesting 2 thread mpi processes each with 12 openmp threads, hence a total of 24 threads however even with hyper threading enabled there are only 12 threads on your machine. Therefore, only allocate 12. Try mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test or even mdrun -v -deffnm md_CaM_test I believe it should autodetect the GPUs and run accordingly for details of how to use gromacs with mpi/thread mpi openmp and GPUs see http://www.gromacs.org/Documentation/Acceleration_and_parallelization Which describes how to use these systems Richard How it could be fixed? All gpu are recognized correctly 2 GPUs detected: #0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC: no, stat: compatible James 2013/11/4 Szilárd Páll pall.szil...@gmail.com You can use the -march=native flag with gcc to optimize for the CPU your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge CPUs. -- Szilárd Páll On Mon, Nov 4, 2013 at 12:37 PM, James Starlight jmsstarli...@gmail.com wrote: Szilárd, thanks for suggestion! What kind of CPU optimisation should I take into account assumint that I'm using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12 nodes in Debian). James 2013/11/4 Szilárd Páll pall.szil...@gmail.com That should be enough. You may want to use the -march (or equivalent) compiler flag for CPU optimization. Cheers, -- Szilárd Páll On Sun, Nov 3, 2013 at 10:01 AM, James Starlight jmsstarli...@gmail.com wrote: Dear Gromacs Users! I'd like to compile lattest 4.6 Gromacs with native GPU supporting on my i7 cpu with dual GeForces Titans gpu mounted. With this config I'd like to perform simulations using cpu as well as both gpus simultaneously. What flags besides cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5 should I define to CMAKE for compiling optimized gromacs on such workstation? Thanks for help James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Re: [gmx-users] Re: Using gromacs on Rocks cluster
You need to configure your MPI environment to do so (so read its docs). GROMACS can only do whatever that makes available. Mark On Tue, Nov 5, 2013 at 2:16 AM, bharat gupta bharat.85.m...@gmail.comwrote: Hi, I have installed Gromcas 4.5.6 on Rocks cluster 6.0 andmy systme is having 32 processors (cpu). But while running the nvt equilibration step, it uses only 1 cpu and the others remain idle. I have complied the Gromacs using enable-mpi option. How can make the mdrun use all the 32 processors ?? -- Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Hardware for best gromacs performance?
Yes, that has been true for GROMACS for a few years. Low-latency communication is essential if you want a whole MD step to happen in around 1ms wall time. Mark On Nov 5, 2013 11:24 PM, Dwey Kauffman mpi...@gmail.com wrote: Hi Szilard, Thanks. From Timo's benchmark, 1 node142 ns/day 2 nodes FDR14 218 ns/day 4 nodes FDR14 257 ns/day 8 nodes FDR14 326 ns/day It looks like a infiniband network is required in order to scale up when running a task across nodes. Is it correct ? Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012280.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0
On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta bharat.85.m...@gmail.comwrote: Hi, I am trying to install gromacs 4.5.7 on rocks cluster(6.0) and it works fine till .configure command, but I am getting error at the make command :- Error: [root@cluster gromacs-4.5.7]# make These is no need to run make as root - doing so guarantees you have almost no knowledge of the final state of your entire machine. /bin/sh ./config.status --recheck running CONFIG_SHELL=/bin/sh /bin/sh ./configure --enable-mpi LDFLAGS=-L/opt/rocks/lib CPPFLAGS=-I/opt/rocks/include --no-create --no-recursion checking build system type... x86_64-unknown-linux-gnu checking host system type... x86_64-unknown-linux-gnu ./configure: line 2050: syntax error near unexpected token `tar-ustar' ./configure: line 2050: `AM_INIT_AUTOMAKE(tar-ustar)' make: *** [config.status] Error 2 Looks like the system has an archaic autotools setup. Probably you can comment out the line with tar-ustar from the original configure script, or remove tar-ustar. Or use the CMake build. I have another query regarding the gromacs that comes with the Rocks cluster distribution. The mdrun of that gromacs has been complied without mpi option. How can I recomplie with mpi option. As I need the .configure file which is not there in the installed gromacs folder of the rocks cluster ... The 4.5-era GROMACS installation instructions are up on the website. Whatever's distributed with Rocks is more-or-less irrelevant. Mark Thanks in advance for help Regards Bharat -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Help to simulate gas mixture
The principle is the same as at http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents On Nov 3, 2013 6:55 PM, ali.nazari ali.nazari.a...@gmail.com wrote: Dear Friends, I am just a beginner in using GROMCS-4.6.3 and I want to simulate gas mixture, the same as mixture of O2 and N2, any help(the same as introducing a reference, not GROMACS manual b/c there is no explanation about gas mixture) is appreciated. Kind Regards, Ali -- View this message in context: http://gromacs.5086.x6.nabble.com/Help-to-simulate-gas-mixture-tp5012193.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] probability distribution of bond distance/length
On Fri, Nov 1, 2013 at 4:04 AM, Xu Dong Huang xudonghm...@gmail.com wrote: Dear all, I would like to assess the probability distribution of particle bond distance/length over the entire run, specifically I want to collect possibly a histogram representation or even a regular plot. Would using g_bond be the correct way to obtain the probability distribution? g_bond -h and/or manual chapter 8 are the best places to start. Or is there another function that gets probability distribution specifically. Also, if using g_bond, it will give me an average (I suppose), so how can I get a histogram/data series representation? (I do not want to visualize this result using xmgrace) g_analyze, or your favourite maths/stats software package. P.S I believe someone earlier suggested a link to the data collection reporting procedure, I tried it and changed the .xvg to a .csv, but the data reported in excel format all belongs to 1 single column, which won’t let me make a plot. A plot of two columns, no, but it should let you plot a histogram! Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] GMX manually generate topology for residues
They're http://en.wikipedia.org/wiki/C_preprocessor symbols that are #defined elsewhere in the directory that contains that .rtp file. The names/symbols probably map to the original force field literature. grep is your friend. Mark On Fri, Nov 1, 2013 at 6:45 AM, charles char...@mails.bicpu.edu.in wrote: i am a newbie to gromacs, trying to generate a new rtp entry for my residue. Bonds, dihedrals of .rtp file has gb_XX what is gb_XX numbers? how can get informations about that? How to define those velues for my residues? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
On Oct 29, 2013 1:26 AM, Pavan Ghatty pavan.grom...@gmail.com wrote: Now /afterok/ might not work since technically the job is killed due to walltime limits - making it not ok. Hence use -maxh! Mark So I suppose /afterany/ is a better option. But I do appreciate your warning about spamming the queue and yes I will re-read PBS docs. On Mon, Oct 28, 2013 at 5:11 PM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. That's why I suggested -maxh, so you can have an orderly shutdown. (Though if a job can get suspended, that won't always help, because mdrun can't find out about the suspension...) Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. Sure - read your PBS docs and find the environment variable to read so that job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on it. But don't tell your sysadmins where I live. ;-) Seriously, if you live on this edge, you could spam infinite jobs, which tends to get your account cut off. That's why you want the afterok hold - you only want the next job to start if the exit code from the first script correctly indicates that mdrun exited correctly. Test carefully! Mark But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow
Re: [gmx-users] pbc problem
On Tue, Oct 29, 2013 at 5:02 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Very thanks for your reply To make this clear, center the trajectory on the water and watch the time evolution in some visualization program. I did your suggestion (center the trajectory on the water). Again, drug molecule is in region (1)in some frames and is in region (4) in other frames. With pbc = xyz, you do not have two chunks of water. You have one chunk of water. Where you put the box for visualization is irrelevant to the simulation. You could align one of the box sides with one of the membrane surfaces, and now you will see only one chunk of membrane, and one chunk of water. In that chunk of water the drug goes wherever diffusion takes it, just like it did inside the membrane. Mark -- Dear Justin Very thanks for your attention As has already been stated several times, there is no problem at all. The outcome is completely normal, and there are not discrete regions (1) and (4). It is a continuous block of water via PBC. The molecule can freely diffuse throughout it. If outcome is completely normal, Can I use this structure for pmf calculation. I want to calculate potential of mean force, delta G, as a function of the distance between the centers of mass of drug and the centers of mass of bilayer. Best wishes for you. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.comwrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Failure in MD run without any error
Hi, Hard to know. LAM was discontinued over 4 years ago. You could have a flaky file system. Unless you're trying to run a jobsover both machines over network like Infiniband, you don't even want to use an external MPI library - single-node performance with built-in thread-MPI will give much better value. Mark On Mon, Oct 28, 2013 at 9:12 PM, niloofar niknam niloofae_nik...@yahoo.comwrote: DearGromacs users I have encountered something strange. I have installed Red Hat Enterprise Linux 6.1 6.2 on two machines recently and then lam 7.1.4, fftw 3.3.2 and Gromacs 4.5.5 . During linux installation, everything went well I didn`t face any complain or receiving any error, as well as in lam, fftw and Gromacs installation, But when I run an MD job on both of these machines, at first everything seems normal but after some steps ( usually multi thousands steps), the job doesn`t proceed. Log file does not show any change or there is no error. Obviously the job is stopped while terminal shows all the processors are 100% busy. I have also reinstalled the linux and the mentioned programs too but it did not solve the problem. I don`t have any idea what the problem is. Any comment or suggestion would be highly appreciated. Thanks in advance, Niloofar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mdrun cpt
On Mon, Oct 28, 2013 at 7:53 PM, Pavan Ghatty pavan.grom...@gmail.comwrote: Mark, The problem with one .tpr file set for 100ns is that when job number (say) 4 hits the wall limit, it crashes and never gets a chance to submit the next job. So it's not really automated. That's why I suggested -maxh, so you can have an orderly shutdown. (Though if a job can get suspended, that won't always help, because mdrun can't find out about the suspension...) Now I could initiate job 5 before /mdrun/ in job 4's script and hold job 5 till job 4 ends. Sure - read your PBS docs and find the environment variable to read so that job 4 knows its ID so it can submit job 5 with an afterok hold on job 4 on it. But don't tell your sysadmins where I live. ;-) Seriously, if you live on this edge, you could spam infinite jobs, which tends to get your account cut off. That's why you want the afterok hold - you only want the next job to start if the exit code from the first script correctly indicates that mdrun exited correctly. Test carefully! Mark But the PBS queuing system is sometime weird and takes a bit of time to recognize a job and give back its jobID. So I could submit job 5 but be unable to change its status to /hold/ because PBS does not return its ID. Another problem is that if resources are available, job 5 could start before I ever get a chance to /hold/ it. On Mon, Oct 28, 2013 at 11:47 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Mon, Oct 28, 2013 at 4:27 PM, Pavan Ghatty pavan.grom...@gmail.com wrote: I have need to collect 100ns but I can collect only ~1ns (1000steps) per run. Since I dont have .trr files, I rely on .cpt files for restarts. For example, grompp -f md.mdp -c md_14.gro -t md_14.cpt -p system.top -o md_15 This runs into a problem when the run gets killed due to walltime limits. I now have a .xtc file which has run (say) 700 steps and a .cpt file which was last written at 600th step. You seem to have no need to use grompp, because you don't need to use a workflow that generates multiple .tpr files. Do the equivalent of what the restart page advises: mdrun -s topol.tpr -cpi state.cpt. Thus, make a .tpr for the whole 100ns run, and then keep doing mdrun -s whole-run -cpi whateverwaslast -deffnm whateversuitsyouthistime with or without -append, perhaps with -maxh, keeping whatever manual backups you feel necessary. Then perhaps concatenate your final trajectory files, according to your earlier choices. - To set up the next run I use the .cpt file from 600th step. - Now during analysis if I want to center the protein and such, /trjconv/ needs an .xtc and .tpr file but not a .cpt file. So how does /trjconv/ know to stop at 600th step? trjconv just operates on the contents of the trajectory file, as modified by things like -b -e and -dt. The .tpr just gives it context, such as atom names. You could give it a .tpr from any point during the run. Mark If this has to be put in manually, it becomes cumbersome. Thoughts? On Sun, Oct 27, 2013 at 11:38 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/27/13 9:37 AM, Pavan Ghatty wrote: Hello All, Is there a way to make mdrun put out .cpt file with the same frequency as a .xtc or .trr file. From here http://www.gromacs.org/**Documentation/How-tos/Doing_**Restarts http://www.gromacs.org/Documentation/How-tos/Doing_RestartsI see that we can choose how often (time in mins) the .cpt file is written. But clearly if the frequency of output of .cpt (frequency in mins) and .xtc (frequency in simulation steps) do not match, it can create problems during analysis; especially in the event of frequent crashes. Also, I am not storing .trr file since I dont need that precision. I am using Gromacs 4.6.1. What problems are you experiencing? There is no need for .cpt frequency to be the same as .xtc frequency, because any duplicate frames should be handled elegantly when appending. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-users http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Search http://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 15
On Mon, Oct 28, 2013 at 8:04 PM, Hari Pandey hariche...@yahoo.com wrote: Dear Gromacs Users, First, I would like to thank Dr. Lemkul for reply. My problem description is as follows: I am using CHARMM36 forcefield to equilibrate of AOT. when I add the mass of all atoms from topology, it gives me 444.5 which is correct but when I run the script Justin asked you about your atom names, but somehow you have forgotten to answer him :-) editconf -c -f A.gro -o A.gro -density 1000 -bt cubic -box 5 -d 0.1 . It display incorrect value for mass of input. The mass of input should be 444.5 . The out come of above script is: Volume: 125 nm^3, corresponds to roughly 56200 electrons No velocities found system size : 0.215 0.234 0.157 (nm) diameter: 0.287 (nm) center : 2.500 2.500 2.500 (nm) box vectors : 5.000 5.000 5.000 (nm) box angles : 90.00 90.00 90.00 (degrees) box volume : 125.00 (nm^3) WARNING: masses and atomic (Van der Waals) radii will be determined based on residue and atom names. These numbers can deviate from the correct mass and radius of the atom type. editconf only has a .gro file, so it does not know about any atom types, or bonds, so it is not worth trying to write code to guess correctly whether HG1 is the first hydrogen on the gamma carbon, or the first mercury, etc. We do write a warning message, but sometimes people don't read them. Mark Volume of input 125 (nm^3) Massof input 967.25 (a.m.u.) Density of input 12.8493 (g/l) Scaling all box vectors by 0.234221 new system size : 0.050 0.055 0.037 shift : 1.914 1.914 1.914 (nm) new center : 2.500 2.500 2.500 (nm) new box vectors : 5.000 5.000 5.000 (nm) new box angles : 90.00 90.00 90.00 (degrees) new box volume : 125.00(nm^3) Here we can see that mass of input is 967.25 which is far beyond the reality. this will cause error in density and all other mass dependent parameters. Please help me how do I come over to this error Thank you so much for you kind help Hari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with reading AMBER trajectories
Hi, Seems plausible, and it's good to know you have the plugins working for at least one format! The question of whether the plugins are out of step with the main VMD distribution would be best raised on the VMD mailing list (but search first!). If you do, you might also suggest that the links in the plugin docs be updated to http://ambermd.org/formats.html Cheers, Mark On Oct 26, 2013 9:20 AM, anu chandra anu80...@gmail.com wrote: Hi, FYI, when I feed the coordinates in '.binpos' format, which I generated after loading the same '.crd' file to VMD, could able to do the job. What I infer from this is that the VMD molfile, for reading AMBER '.crd' trajectories, has made for reading AMBER 7 '.crd' formatted trajectories which can not able to read latest ones. On Sat, Oct 26, 2013 at 12:21 PM, anu chandra anu80...@gmail.com wrote: Hi, Sorry for the late reply. I have tried all the possibilities with filename extension as mentioned in the VMD molfile details. As said, VMD uses .crd or .crdbox filename extensions for reading Amber trajectories. I have tried with both the options ( ie. with .crd and .crdbox extensions) , but unfortunately both the attempt got failed with same error as shown below * Note: the fit and analysis group are identical, while the fit is mass weighted and the analysis is not. Making the fit non mass weighted. WARNING: If there are molecules in the input trajectory file that are broken across periodic boundaries, they cannot be made whole (or treated as whole) without you providing a run input file. Calculating the average structure ... The file format of eqc.crdbox is not a known trajectory format to GROMACS. Please make sure that the file is a trajectory! GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins. This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. Using VMD plugin: crdbox (AMBER Coordinates with Periodic Box) Format of file eqc.crdbox does not record number of atoms. --- Program g_covar, VERSION 4.6.1 Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035 Fatal error: Not supported in read_first_frame: md1.crdbox For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Hang On to Your Ego (F. Black) Can anyone please help me to figure out what is going wrong here? Many thanks Anu On Fri, Oct 18, 2013 at 6:21 PM, Mark Abraham mark.j.abra...@gmail.com wrote: OK. All GROMACS does is feed your filename extension to the VMD library and let it choose how to read the file based on that. If that doesn't make sense (and it seems it doesn't, because GROMACS wasn't told about the number of atoms, and it needs to know), then the ball is back to you to choose the filename extension in the way the plugin needs. I suggest you check out http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ and try some alternatives. Mark On Fri, Oct 18, 2013 at 2:10 PM, anu chandra anu80...@gmail.com wrote: Hi Mark, Yes. I do can able to load the trajectories successfully in VMD with the file format option of ' AMBER coordinate with periodic box'. I am using VMD 1.9 version. Regards Anu On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Can this file be opened in VMD itself? Mark On Oct 18, 2013 6:21 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few analysis. Unfortunately I ended-up with the following error. GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins. This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. Using VMD plugin: crd (AMBER Coordinates) Format of file md.crd does not record number of atoms. --- Program g_covar, VERSION 4.6.1 Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035 Fatal error: Not supported in read_first_frame: md.crd For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors
Re: [gmx-users] Re: gmx-users Digest, Vol 114, Issue 64
On Sat, Oct 26, 2013 at 2:07 PM, Santu Biswas santu.biswa...@gmail.comwrote: Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- Thanks Mark for your reply. Using the 500ps trajectory i want to calculate the number of hydrogen bonds as a function of time in vacuum .For this calculation i have uesd g_hbond_d -f traj_0-500ps.trr -s 500ps.tpr -n index.ndx -num hbond-num.xvg -dist dist.xvg -ang angle.xvg With what groups? Can there be any hydrogen bonds between those groups? Is there a bug fixed in a version of g_hbond that isn't 2 years old? Did a shorter trajectory work because it took less time? Does doing only one of three analyses help things to work? You'd be much closer to a solution if you'd tried some simplifications and done some detective work already ;-) Programm was running .After 1 hour it was still running but there was no output. If I calculate the number of hydrogen bonds as a function of time in water (no vacuum) using the same command line then there was no problem. Same problem when I used g_rdf in vacuum.The commad line I have used g_rdf_4.5.5 -f traj.trr -s 500ps.tpr -n index.ndx -o rdf.xvg and also checked with -nopbc with the same command line. RDF of what, in vacuum? What groups did you use? The programm is running but in the output file nothing is written. If I used g_rdf in water using the same command line there was no problem. OK - but does your analysis make sense in vacuum? Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Optimizing performance mac osx
On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes tiagogome...@gmail.comwrote: Hi, I am relatively new to the gromacs environment and would like to optimize performance for my mac pro (osx 10.6.8) with 8 cores (16 in hyper-theading). I´ve read that one can use the g_tune_pme, i guess with np = 16. Don´t know if using mpirun or gromacs compiled mpi would be faster. Won't be. GROMACS's default built-in thread-MPI is designed for this case. Do check out http://www.gromacs.org/Documentation/Acceleration_and_parallelization I guess sin gromacs 4,5 mpirun is deprecated and mdrun automatically distributes the workload through all the cores, i think. We also have a 40 core condor cluster; would setting it up there increase performance? Using more than one node for the same simulation is not useful unless you have a high-speed network, e.g. Infiniband. A network over which one would use Condor would generally not be suitable. I think also that the scaling depends on the number of atoms. Any info on this? Depends very much on the hardware, compiler, model physics and simulation composition, also. You should aim for something at least around 500-800 atoms per physical core, though. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
On Oct 24, 2013 8:10 AM, shahab shariati shahab.shari...@gmail.com wrote: Dear jkrieger I used 2 times trjconv tool: 1) trjconv -f npt.xtc -s npt.tpr -n index.ndx -o 2npt.xtc -pbc nojump 2) trjconv -f 2npt.xtc -s npt.tpr -n index.ndx -o 3npt.xtc -pbc mol -center Dear Mark I selected all lipid atoms for centering. With my manner, pbc problem was solved just for lipids and not for drug molecule which is put inside water molecules in top leaflet. This pbc problem cause to drug molecule be in top and bottom leaflets, while I want to study translocation of the drug molecule from water to lipid bilayer. I want to solve this problem for drug molecule. There is only one water region, so upper and lower don't mean much. If you just want to see the drug and bilayer in the same PBC cell, then center on something that is central. Mark If my manner is wrong, please tell me true way. Best wishes. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] g_hbond and g_rdf in vacuum
Not working is too vague a symptom for anyone to guess what the problem is, sorry. Mark On Oct 24, 2013 9:39 AM, Santu Biswas santu.biswa...@gmail.com wrote: dear users, I am performing 500ps mdrun in vacuum for polypeptide(formed by 10-residues leucine) using gromacs_4.5.5(double-precision) using opls-aa/L force field.Input file for 500ps mdrun is given below title= peptide in vaccum cpp= /lib/cpp ; RUN CONTROL integrator = md comm_mode= ANGULAR nsteps = 50 dt= 0.001 ; NEIGHBOR SEARCHING nstlist = 0 ns_type = simple pbc = no rlist = 0 ; OUTPUT CONTROL nstxout = 1000 nstvout = 1000 nstxtcout = 0 nstlog= 1000 constraints = none nstenergy = 1000 ; OPTION FOR ELECTROSTATIC AND VDW rcoulomb = 0 ; Method for doing Van der Waals rvdw= 0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS tcoupl = V-rescale tc_grps= Protein tau_t= 0.1 ref_t = 300 gen_vel= yes gen_temp = 300 Using the 500ps trajectory if i run g_hbond_d for calculating the number of hydrogen bonds as a function of time using index file(where atom O and atom N H is used) it is not working. Also if i used g_rdf_d with pbc=no using the 500ps trajectory it is also not working. I do not know why this is happening. -- santu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output pinning for mdrun
Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. What question were you seeking to answer? Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Output pinning for mdrun
On Thu, Oct 24, 2013 at 4:52 PM, Carsten Kutzner ckut...@gwdg.de wrote: On Oct 24, 2013, at 4:25 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Hi, No. mdrun reports the stride with which it moves over the logical cores reported by the OS, setting the affinity of GROMACS threads to logical cores, and warnings are written for various wrong-looking cases, but we haven't taken the time to write a sane report of how GROMACS logical threads and ranks are actually mapped to CPU cores. Where supported by the processor, the CPUID information is available and used in gmx_thread_affinity.c. It's just not much fun to try to report that in a way that will make sense on all possible hardware that supports CPUID - and then people will ask why it doesn't map to what their mpirun reports, get confused by hyper-threading, etc. Yes, I see. What question were you seeking to answer? Well, I just wanted to check whether my process placement is correct and that I am not getting decreased performance due to a suboptimal placement. In many cases the performance is really bad (like 50% of the expected values) if the pinning is wrong or does not work, but you never know. GROMACS does report if its attempt to set affinities fail (and the reason), which covers some of the problem cases. Keeping MPI ranks closely associated with the hardware granularity (nodes, sockets, GPUs) will be important, but that's something to configure at the mpirun level. (Thread-MPI, being a single-node solution, has more assumptions it can make safely.) Keeping OpenMP threads within their MPI ranks pinned within hardware regions is important, but severity and solutions vary a lot with the hardware and software context (e.g. you might as well get out an abacus, as run GROMACS with OpenMP spread over a whole AMD processor, but with a single GPU then that can be the best you can do, at the moment). Key to interpreting performance results is to measure the (pinned) single-core performance, so that there is a minimum-overhead reference number for comparison. Mark On some clusters there are of course tools that check and output the process placement for a dummy parallel job, or environment variables like MP_INFOLEVEL for loadleveler. Thanks! Carsten Mark On Thu, Oct 24, 2013 at 11:44 AM, Carsten Kutzner ckut...@gwdg.de wrote: Hi, can one output how mdrun threads are pinned to CPU cores? Thanks, Carsten -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] nstcalclr bug?
Ja. No twin-range = no long-range :-) Mark On Thu, Oct 24, 2013 at 5:50 PM, jkrie...@mrc-lmb.cam.ac.uk wrote: I think nstcalclr would only do something if you have longer range interactions to calculate (lr means longer than rlist). Therefore something has be longer than rlist for this to happen. Hi there, I am using gromacs-4.6.1 with this mdp file: integrator= md; leap-frog integrator nsteps= 300 ; 6.0 ns dt= 0.002 ; 2 fs nstxout = 0 ; save coordinates every 10 ps nstvout = 0 ; save velocities every 10 ps nstenergy = 5000 ; save energies every 10 ps nstlog= 5000 ; update log file every 5 ps nstcalcenergy = 100 ; nstxtcout = 5000 ; xtc every 10 ps xtc_precision = 100 continuation = yes ; Restarting constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ns_type = grid ; search neighboring grid cells nstlist = 20; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) nstcalclr= 10 cutoff-scheme = Group vdwtype = Cut-off vdw-modifier = Potential-shift coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing= 0.16 ; grid spacing for FFT coulomb-modifier = Potential-shift tcoupl= V-rescale ; modified Berendsen thermostat tc-grps = System; two coupling groups - more accurate tau_t = 0.1 ; time constant, in ps ref_t = 300 ; reference temperature, one for each group, in K energygrps = complex Water; group(s) to write to energy file pcoupl= Parrinello-Rahman ; Pressure coupling on in NPT pcoupltype= isotropic ; uniform scaling of box vectors tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 refcoord_scaling = com pbc = xyz ; 3-D PBC DispCorr = EnerPres ; account for cut-off vdW scheme gen_vel = no; Velocity generation is off gen-seed= 128742 ; number of steps for center of mass motion removal nstcomm = 1000 the mdout.mdp file says nstcalclr = 10, but gmxdump of the tpr file says nstcalclr = 0. If I set rvdw = 1.4 ( rlist), gmxdump of the file tpr is now correct to nstcalclr = 10. I have double checked the manual but I couldn't find the reason of this behaviour. is this a bug or am I doing wrong somewhere?? thanks for any helps and Andrea Spitaleri PhD D3 - Drug Discovery Development Istituto Italiano di Tecnologia Via Morego, 30 16163 Genova cell: +39 3485188790 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
As Justin said, there is no actual division between region 1 and 4. Apparently you got the free diffusion you asked for! :-) Mark On Thu, Oct 24, 2013 at 4:57 PM, shahab shariati shahab.shari...@gmail.comwrote: Dear Mark Thank for your reply. If I show my system as 4 regions, my system before equilibration is as fallows: region (1): water + drug region (2): top leaflet of bilayer region (3): bottom leaflet of bilayer region (4): water After equilibration, drug molecule exits region (1) and enters region (4). Please tell me how to fix it? Which options of trjconv are appropriate for this problem? Best wishes -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Continuing runs from 4.5.4 in 4.6.3
On Oct 23, 2013 7:24 AM, rajat desikan rajatdesi...@gmail.com wrote: Hi, We recently had a software upgrade in our cluster from gromacs 4.5.4. to gromacs 4.6.3.. I need to continue an earlier simulation that had been run in 4.5.4. using the .cpt, .tpr and .mdp. Are there any issues with continuing these runs in 4.6.3.? Can I concatenate these trajectories for later analysis? This is not recommended. Even if it works, the trajectory is discontinuous, and the years of accumulated bug fixes, and complete re-implementation of the kernels in 4.6.3, are likely to make the discontinuity observable. Upgrading within a minor release (4.5.4 - 4.5.7, 4.6 - 4.6.3) is intended to work (modulo relevant bug fixes), but would still tend to make your reviewer nervous. Mark I notice that I cannot use a 4.6.3 .cpt and .tpr in 4.5.4. Any input will be appreciated. Thanks. -- Rajat Desikan (Ph.D Scholar) Prof. K. Ganapathy Ayappa's Lab (no 13), Dept. of Chemical Engineering, Indian Institute of Science, Bangalore -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box size increases in NPT
On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely to have occurred without crashing. Over what time span? How did you observe before and after? What densities do you measure? Mark I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Box size increases in NPT
By crash I meant explode not DD is impossible. Explosions don't happen because of parallelism, they happen because the steps are too large for the size of the forces. The forces required to stably expand a box from 20A to 70A seem likely to be so large that I am very skeptical that you could design such a simulation to do this with a 1fs time step. Mark On Wed, Oct 23, 2013 at 11:39 AM, Dr. Vitaly Chaban vvcha...@gmail.comwrote: If the job is not very parallel, it will not crash. It is better to preequilibrate in NVT beforehand. Cyclopropylchloride is probably a liquid at 290K, if the model is parametrized reasonably. So it should not phase-separate. Vitaly On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham mark.j.abra...@gmail.com wrote: On Oct 23, 2013 5:34 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Hello, I am running a NPT simulation for cyclopropylchloride(1) in 50%water(100)+50%ethanol(100) using opls force field parameter . After equilibration box size increases from 20 A to 70 A. Really? Seems wildly unlikely to have occurred without crashing. Over what time span? How did you observe before and after? What densities do you measure? Mark I used the following mdp file. ; RUN CONTROL PARAMETERS = integrator = sd ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 5 ; number of steps for center of mass motion removal = nstcomm = 100 ; OUTPUT CONTROL OPTIONS = ; Output frequency for coords (x), velocities (v) and forces (f) = nstxout = 0 nstvout = 0 nstfout = 0 ; Output frequency for energies to log file and energy file = nstlog = 500 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 5000 xtc-precision= 1000 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ;OPTIONS FOR TEMPERATURE COUPLING tc_grps = system tau_t= 0.1 ref_t= 290;350 ;OPTIONS FOR PRESSURE COUPLING Pcoupl = berendsen tau_p= 0.5 compressibility = 4.5e-05 ref_p= 1.0 ; OPTIONS FOR BONDS = constraints = hbonds ; Type of constraint algorithm = constraint-algorithm = Lincs ; Do not constrain the start configuration = unconstrained-start = no ; Relative tolerance of shake = shake-tol= 0.0001 ; Highest order in the expansion of the constraint coupling matrix = lincs-order = 12 ; Lincs will write a warning to the stderr if in one step a bond = ; rotates over more degrees than = lincs-warnangle = 30 ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist= 0.9 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = pme ;rcoulomb-switch = 0 rcoulomb = 0.9 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon-r= 1 ; Method for doing Van der Waals = vdw-type = switch ; cut-off lengths= rvdw-switch = 0.8 rvdw = 0.9 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = EnerPres ; Spacing for the PME/PPPM FFT grid = fourierspacing = 0.1 ; FFT grid size, when a value is 0 fourierspacing will be used = fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters = pme_order= 6 ewald_rtol = 1e-06 epsilon_surface = 0 optimize_fft = no ; Free energy control stuff free_energy = no Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] a new GROMACS simulation tool
Hi, Sounds very interesting. Can I have a test account, please? The Lindahl group has some related work going on at http://copernicus-computing.org/, automating large-scale simulation workflows. I'm not sure yet whether we have any synergies! :-) Cheers, Mark On Tue, Oct 22, 2013 at 4:34 PM, Kevin Chen fch6...@gmail.com wrote: Hi Everyone, I'm writing to let you guys know that we have developed a web-based tool MD simulation tool for GROMACS. It is a software package primarily developed for biological MD and offers a huge amount of possible options and settings for tailoring the simulations. Seamlessly integrated with newly developed GUI interfaces, the tool provides comprehensive setup, simulation, analysis and job submission tools. Most importantly, unlike other GROMACS GUI applications, user can actually run really simulations using the dedicated HPC resources. That been said, there's no proposal and installation required. This tool could be a great fit for both teaching and research projects. Users inexperienced in MD can work along prepared workflows, while experts may enjoy a significant relief from the tedium of typing and scripting. As for now, we'd like to invite people to participate in user testing on this newly developed tool. Let me know if you'd like to try it out. We will set up an account for you. Best Regards, Kevin Chen, Ph.D. Information Technology at Purdue (ITaP) West Lafayette, IN 47907-2108 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] pbc problem
Center on a particular lipid? Or head group? Mark On Oct 23, 2013 6:13 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear gromacs users My system contains DOPC + CHOLESTEROLO + WATER + drug molecules in a rectangular box. I put drug molecule in 2 position: a) drug in the center of bilayer membrane, b) drug inside water molecules in top leaflet. For both positions, I did energy minimization successfully with following mdp file. -- ; Parameters describing what to do, when to stop and what to save integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 1000.0 ; Stop minimization when the maximum force 1000.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions --- After energy minimization, I saw obtained file (em.gro) by VMD. All things were true and intact. For both positions, I did equilibration in NPT ensemble with following mdp file. --- ; Run parameters integrator= md; leap-frog integrator nsteps= 25; 2 * 50 = 1000 ps (1 ns) dt= 0.002; 2 fs ; Output control nstxout= 100; save coordinates every 0.2 ps nstvout= 100; save velocities every 0.2 ps nstxtcout = 100; xtc compressed trajectory output every 2 ps nstenergy= 100; save energies every 0.2 ps nstlog= 100; update log file every 0.2 ps energygrps = CHOL DOPC drg SOL ; Bond parameters continuation= no; Restarting after NVT constraint_algorithm = lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching ns_type= grid; search neighboring grid cels nstlist= 5; 10 fs rlist= 1.0; short-range neighborlist cutoff (in nm) rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; More accurate thermostat tc-grps= CHOL_DOPCdrg SOL; three coupling groups - more accurate tau_t= 0.50.5 0.5 ; time constant, in ps ref_t= 323 323 323 ; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= semiisotropic; uniform scaling of x-y box vectors, independent z tau_p= 5.0; time constant, in ps ref_p= 1.01.0; reference pressure, x-y, z (in bar) compressibility = 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= yes; assign velocities from Maxwell distribution gen_temp= 323; temperature for Maxwell distribution gen_seed= -1; generate a random seed ; COM motion removal ; These options remove motion of the protein/bilayer relative to the solvent/ions nstcomm = 1 comm-mode = Linear comm-grps = CHOL_DOPC_drg SOL ; Scale COM of reference coordinates refcoord_scaling = com --- For 2 positions, I chechked tempreture and pressure fluctuation and box dimention during equilibration. All things were good. When I saw trajectory by VMD (npt.gro and npt xtc), I had pbc problem (some atoms leave box and enter the box in opposit direction). For
Re: [gmx-users] regarding charge group
Probably, make your broken molecules whole before passing them to grompp. Mark On Tue, Oct 22, 2013 at 8:26 AM, Sathish Kumar sathishk...@gmail.comwrote: The sum of the two largest charge group radii (13.336) is larger than rlist(1.2) - rvdw/rcoulomb i am getting this error while running membrane simulations. please any one suggest how to rectify this error. -- regards M.SathishKumar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Ligand breaking in to two
Sounds like issues with http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions, strategies for coping found there. Mark On Mon, Oct 21, 2013 at 9:31 AM, MUSYOKA THOMMAS mutemibiochemis...@gmail.com wrote: Dear Users, I am doing protein-ligand MD simulations. I first prepare the ligand by adding Hydrogen atoms and setting the charges using UCSF chimera. I thereafter use acpype to get the ligand's gro,itp and top files. Finally, i process the protein.PDB file and perform MD simulations. However, when I combine the ligand and protein gro files and convert the resulting complex to a PDB file so as to visualise with VMD, the ligand always appears to be broken in two parts. Any advice on how to overcome this? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Insertion of chromium III ion into lipid bilayer
First, can you successfully add an ion that the force field already knows about, like potassium? Second, does the force field know about chromium? If not, who does? Mark On Sat, Oct 19, 2013 at 4:27 PM, Sathya bti027.2...@gmail.com wrote: Hi, I want to add chromium III ion into lipid bilayer. I have included cr entry in the ions.itp file, and I used grompp it shows error like Atom types cr+3 is not found. After removing cr ions from the ions.itp file it works and after using genion to add cr3+ ions into lipid the following command was used. genion -s ions.tpr -o dppc_solv_ions.gro -p topol.top -pname CR -pq 3 But it shows No ions to add and no potential to calculate.. Is it necessary to include chromium entry in the ions.itp file? What file i should modify to add cr into lipid? Please explain me to solve this.. Thanks -- View this message in context: http://gromacs.5086.x6.nabble.com/Insertion-of-chromium-III-ion-into-lipid-bilayer-tp5011884.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with reading AMBER trajectories
Can this file be opened in VMD itself? Mark On Oct 18, 2013 6:21 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few analysis. Unfortunately I ended-up with the following error. GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins. This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. Using VMD plugin: crd (AMBER Coordinates) Format of file md.crd does not record number of atoms. --- Program g_covar, VERSION 4.6.1 Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035 Fatal error: Not supported in read_first_frame: md.crd For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- While browsing through the GROMACS mail-list, I came to know that it might be a problem with DLOPEN libraries. So I recompiled Gromcas with cmake using the following command CMAKE_PREFIX_PATH=/usr/include/libltdl cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DFFTWF_LIBRARY=/usr/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/usr/lib/ ../ But, the same problem came-up again. Can anyone help me to figure out what went wrong with my Gromacs installation? Many thanks in advance. Regards Anu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Problem with reading AMBER trajectories
OK. All GROMACS does is feed your filename extension to the VMD library and let it choose how to read the file based on that. If that doesn't make sense (and it seems it doesn't, because GROMACS wasn't told about the number of atoms, and it needs to know), then the ball is back to you to choose the filename extension in the way the plugin needs. I suggest you check out http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ and try some alternatives. Mark On Fri, Oct 18, 2013 at 2:10 PM, anu chandra anu80...@gmail.com wrote: Hi Mark, Yes. I do can able to load the trajectories successfully in VMD with the file format option of ' AMBER coordinate with periodic box'. I am using VMD 1.9 version. Regards Anu On Fri, Oct 18, 2013 at 1:05 PM, Mark Abraham mark.j.abra...@gmail.com wrote: Can this file be opened in VMD itself? Mark On Oct 18, 2013 6:21 AM, anu chandra anu80...@gmail.com wrote: Dear Gromacs users, I am trying to use Gromacs to read AMBER trajectories (mdcrd) for doing few analysis. Unfortunately I ended-up with the following error. GROMACS will now assume it to be a trajectory and will try to open it using the VMD plug-ins. This will only work in case the VMD plugins are found and it is a trajectory format supported by VMD. Using VMD plugin: crd (AMBER Coordinates) Format of file md.crd does not record number of atoms. --- Program g_covar, VERSION 4.6.1 Source code file: /usr/local/gromacs-4.6.1/src/gmxlib/trxio.c, line: 1035 Fatal error: Not supported in read_first_frame: md.crd For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- While browsing through the GROMACS mail-list, I came to know that it might be a problem with DLOPEN libraries. So I recompiled Gromcas with cmake using the following command CMAKE_PREFIX_PATH=/usr/include/libltdl cmake -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DFFTWF_LIBRARY=/usr/lib/libfftw3f.a -DFFTWF_INCLUDE_DIR=/usr/lib/ ../ But, the same problem came-up again. Can anyone help me to figure out what went wrong with my Gromacs installation? Many thanks in advance. Regards Anu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] mistake occured in Gromacs install
You do need a C compiler, not a Fortran one, and IIRC gcc 4.6.2 has some known issues. Please follow the instructions in the install guide and get the latest compiler you can. Mark On Oct 17, 2013 8:30 AM, 张海平 21620101152...@stu.xmu.edu.cn wrote: Dear professor: When I install the Gromacs software, there occured a problem as follow(my computer is 64bit,linux, gcc is GNU Fortran (GCC) 4.6.2): [ZHP@console build]$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -- No compatible CUDA toolkit found (v3.2+), disabling native GPU acceleration CMake Warning at CMakeLists.txt:744 (message): No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance CMake Error at CMakeLists.txt:767 (message): Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support. -- Configuring incomplete, errors occurred! I don't know how to solve it. Hope your reply soon. Best regards Haiping Zhang -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] default -rdd with distance restraints seems too large
Hi, The log file gives a breakdown of how the minimum cell size was computed. What does it say? Mark On Oct 17, 2013 5:17 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: I have a system that also uses a set of distance restraints The box size is: 7.12792 7.12792 10.25212 When running mdrun -nt 8, I get: Fatal error: There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 3.62419 nm However, the largest restrained distance is 2.0 nm and the largest displacement between restrained atoms is 2.63577 nm So why does mdrun set -rdd to 3.62419 nm ? If I run mdrun -rdd 2.8 everything works fine. Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm
4.5 can only handle about 500-1000 atoms per processor. Details vary. Mark On Oct 17, 2013 5:39 AM, Nilesh Dhumal ndhu...@andrew.cmu.edu wrote: Thanks for you reply. I am doing simulation for ionic liquids BMIM + CL. Total number of atoms are 3328. Nilesh Assuming you're using LINCS, from the manual: With domain decomposition, the cell size is limited by the distance spanned by *lincs-order*+1 constraints. Assuming a default lincs-order (4), 0.82nm seems a fairly sane distance for 5 bonds. Which means that you're probably using too many nodes for the size of your system. Hope that helps. If it doesn't you'll need to provide some information about your system. -Trayder On Thu, Oct 17, 2013 at 1:27 PM, Nilesh Dhumal ndhu...@andrew.cmu.eduwrote: Hello, I am getting the following error for simulation. I am using Gromacs VERSION 4.5.5 and running on 24 processors. Should I reduce the number of processor or the problem is in bonded parameters. If I use -nt 1 option. I could run the simulation. Fatal error: There is no domain decomposition for 16 nodes that is compatible with the given box and a minimum cell size of 0.826223 nm Change the number of nodes or mdrun option -rdd or -dds Look in the log file for details on the domain decomposition Nilesh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102
(Redirected from gmx-developers)
The only way I can reproduce those symptoms is if I delete (or otherwise
make unreadable) various parts of src/gmxlib. You may have deleted some
files or been a different user at some point. I suggest you do a fresh
unpack of the tarball and try again.
Mark
On Wed, Oct 16, 2013 at 7:19 AM, Nikolay Alemasov suc...@gmail.com wrote:
Greetings,
I am trying to compile the source code v.4.6.3 with cmake. The shell
script is (ran from the build directory inside gromacs source root dir):
CC=/ifs/opt/2013/intel/bin/icc
CXX=/ifs/opt/2013/intel/bin/**icpc
CMAKE_PREFIX_PATH=/ifs/home/**bionet/alemasov/libraries/**fftw
cmake .. \
-DGMX_GPU=OFF \
-DGMX_CPU_ACCELERATION=SSE2 \
-DFFTWF_LIBRARY='/ifs/home/**bionet/alemasov/libraries/**fftw/lib/libfftw3f.so'
\
-DFFTWF_INCLUDE_DIR='/ifs/**home/bionet/alemasov/**libraries/fftw/include'
\
-DCMAKE_INSTALL_PREFIX='/ifs/**home/bionet/alemasov/**libraries/gromacs'
And get a message (successful part was cut):
...
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Found the ability to use plug-ins when building shared libaries, so
will compile to use plug-ins (e.g. to read VMD-supported file formats).
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
CMake Error at src/gmxlib/CMakeLists.txt:102 (list):
list sub-command REMOVE_ITEM requires two or more arguments.
CMake Error at src/gmxlib/CMakeLists.txt:105 (list):
list sub-command REMOVE_ITEM requires two or more arguments.
You have called ADD_LIBRARY for library md without any source files. This
typically indicates a problem with your CMakeLists.txt file
-- Configuring incomplete, errors occurred!
See also /ifs/home/bionet/alemasov/**libraries/gromacs-4.6.3/build/**
CMakeFiles/CMakeOutput.log.
See also /ifs/home/bionet/alemasov/**libraries/gromacs-4.6.3/build/**
CMakeFiles/CMakeError.log.
Below is a content of the src/gmxlib/CMakeLists.txt:99-**105:
99 : # Files called xxx_test.c are test drivers with a main() function
for module xxx.c,
100: # so they should not be included in the library
101: file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
102: list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})
103: # Selection has test_ instead of _test.
104: file(GLOB SELECTION_TEST selection/test*)
105: list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
The target system:
Linux nks-g6.sscc.ru 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009
x86_64 x86_64 x86_64 GNU/Linux
Red Hat Enterprise Linux Server release 5.4 (Tikanga)
model name: Intel(R) Xeon(R) CPU X5560 @ 2.80GHz
Please help me to sort out the issue. In fact my primary aim was to build
GPU-version of the GROMACS, but I can not do it even for the simplest
variant.
--
gmx-developers mailing list
gmx-develop...@gromacs.org
http://lists.gromacs.org/**mailman/listinfo/gmx-**developershttp://lists.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to
gmx-developers-request@**gromacs.orggmx-developers-requ...@gromacs.org
.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: [gmx-developers] v4.6.3: cmake-stage error at CMakeLists.txt:102
On Wed, Oct 16, 2013 at 12:27 PM, Nikolay Alemasov suc...@gmail.com wrote:
Thank you, Mark!
It was already tried. I mean a fresh unpacking and further cmake run.
As for your first thought concerning a loss of access to some parts of
gmxlib:
[alemasov@nks-g6 gromacs-4.6.3]$ ls -l ./src/gmxlib/ | grep -e - | cut
-d' ' -f 1 | sort -n | uniq
drwxr-x---
-rw-r-
So there are only two permissions patterns which allow me to
read/write items in the directory. I am little bit confused. Are there any
limitations about OS or cmake versions? The latter is cmake version
2.8.12.
Also relevant are the owners, if you have unpacked as root and built as
normal user, or vice-versa, etc. You should be doing nothing with root
until you need to install, of course, and since you are installing to user
space, you definitely should not be root.
CMake has not yet updated their compatibility matrix for 2.8.12 (
http://www.cmake.org/Wiki/CMake_Version_Compatibility_Matrix/Commands) and
as you can see there, things that used to work occasionally stop working.
If you can try a different version of CMake we can rule out bugs in CMake
2.8.12.
Mark
(Redirected from gmx-developers)
The only way I can reproduce those symptoms is if I delete (or otherwise
make unreadable) various parts of src/gmxlib. You may have deleted some
files or been a different user at some point. I suggest you do a fresh
unpack of the tarball and try again.
Mark
On Wed, Oct 16, 2013 at 7:19 AM, Nikolay Alemasov such3r at gmail.com
http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
wrote:
/ Greetings,
//
// I am trying to compile the source code v.4.6.3 with cmake. The
shell
// script is (ran from the build directory inside gromacs source root
dir):
//
// CC=/ifs/opt/2013/intel/bin/icc
// CXX=/ifs/opt/2013/intel/bin/icpc
// CMAKE_PREFIX_PATH=/ifs/home/bionet/alemasov/libraries/
fftw
//
// cmake .. \
// -DGMX_GPU=OFF \
// -DGMX_CPU_ACCELERATION=SSE2 \
// -DFFTWF_LIBRARY='/ifs/home/bionet/alemasov/libraries/
fftw/lib/libfftw3f.so'
// \
// -DFFTWF_INCLUDE_DIR='/ifs/home/bionet/alemasov/
libraries/fftw/include'
// \
// -DCMAKE_INSTALL_PREFIX='/ifs/home/bionet/alemasov/
libraries/gromacs'
//
//
// And get a message (successful part was cut):
// ...
//
// -- Performing Test HAVE_DLOPEN
// -- Performing Test HAVE_DLOPEN - Success
// -- Checking for dlopen - found
// -- Found the ability to use plug-ins when building shared libaries,
so
// will compile to use plug-ins (e.g. to read VMD-supported file
formats).
// -- Checking for suitable VMD version
// -- VMD plugins not found. Path to VMD can be set with VMDDIR.
// CMake Error at src/gmxlib/CMakeLists.txt:102 (list):
//list sub-command REMOVE_ITEM requires two or more arguments.
//
//
// CMake Error at src/gmxlib/CMakeLists.txt:105 (list):
//list sub-command REMOVE_ITEM requires two or more arguments.
//
//
// You have called ADD_LIBRARY for library md without any source
files. This
// typically indicates a problem with your CMakeLists.txt file
// -- Configuring incomplete, errors occurred!
// See also /ifs/home/bionet/alemasov/
libraries/gromacs-4.6.3/build/
// CMakeFiles/CMakeOutput.log.
// See also /ifs/home/bionet/alemasov/
libraries/gromacs-4.6.3/build/
// CMakeFiles/CMakeError.log.
//
//
// Below is a content of the src/gmxlib/CMakeLists.txt:99-105:
//
// 99 : # Files called xxx_test.c are test drivers with a main()
function
// for module xxx.c,
// 100: # so they should not be included in the library
// 101: file(GLOB_RECURSE NOT_GMXLIB_SOURCES *_test.c *\#*)
// 102: list(REMOVE_ITEM GMXLIB_SOURCES ${NOT_GMXLIB_SOURCES})
// 103: # Selection has test_ instead of _test.
// 104: file(GLOB SELECTION_TEST selection/test*)
// 105: list(REMOVE_ITEM GMXLIB_SOURCES ${SELECTION_TEST})
//
//
// The target system:
//
// Linux nks-g6.sscc.ru 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT
2009
// x86_64 x86_64 x86_64 GNU/Linux
// Red Hat Enterprise Linux Server release 5.4 (Tikanga)
// model name: Intel(R) Xeon(R) CPU X5560 @ 2.80GHz
//
//
// Please help me to sort out the issue. In fact my primary aim was to
build
// GPU-version of the GROMACS, but I can not do it even for the simplest
// variant.
// --
// gmx-developers mailing list
// gmx-developers at gromacs.org http://lists.gromacs.org/**
mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users
//
http://lists.gromacs.org/mailman/listinfo/gmx-developershttp://lists.gromacs.org/**mailman/listinfo/gmx-**developers
http://lists.**gromacs.org/mailman/listinfo/**gmx-developershttp://lists.gromacs.org/mailman/listinfo/gmx-developers
http://lists.gromacs.org/mailman/listinfo/gmx-
Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)
On Thu, Oct 10, 2013 at 2:34 PM, James jamesresearch...@gmail.com wrote: Dear Mark, Thanks again for your response. Many of the regression tests seem to have passed: All 16 simple tests PASSED All 19 complex tests PASSED All 142 kernel tests PASSED All 9 freeenergy tests PASSED All 0 extra tests PASSED Error not all 42 pdb2gmx tests have been done successfully Only 0 energies in the log file pdb2gmx tests FAILED I'm not sure why pdb2gmx failed but I suppose it will not impact the crashing I'm experiencing. No, that's fine. Probably they don't have sufficiently explicit guards to stop people running the energy minimization with a more-than-useful number of OpenMP threads. Regarding the stack trace showing line numbers, what is the best way to go about this, in this context? I'm not really experienced in that aspect. That's a matter of compiling in debug mode (use cmake .. -DCMAKE_BUILD_TYPE=Debug), and hopefully observing the same crash with an error message that has more useful information. The debug mode annotates the executable so that a finger can be pointed at the code line that caused the segfault. Hopefully the compiler does this properly, but support for this in OpenMP is a corner compiler writers might cut ;-) Depending on the details, loading a core dump in a debugger can also be necessary, but your local sysadmins are the people to talk to there. Mark Thanks again for your help! Best regards, James On 21 September 2013 23:12, Mark Abraham mark.j.abra...@gmail.com wrote: On Sat, Sep 21, 2013 at 2:45 PM, James jamesresearch...@gmail.com wrote: Dear Mark and the rest of the Gromacs team, Thanks a lot for your response. I have been trying to isolate the problem and have also been in discussion with the support staff. They suggested it may be a bug in the gromacs code, and I have tried to isolate the problem more precisely. First, do the GROMACS regression tests for Verlet kernels pass? (Run them all, but those with nbnxn prefix are of interest here.) They likely won't scale to 16 OMP threads, but you can vary OMP_NUM_THREADS environment variable to see what you can see. Considering that the calculation is run under MPI with 16 OpenMP cores per MPI node, the error seems to occur under the following conditions: A few thousand atoms: 1 or 2 MPI nodes: OK Double the number of atoms (~15,000): 1 MPI node: OK, 2 MPI nodes: SIGSEGV error described below. So it seems that the error occurs for relatively large systems which use MPI. ~500 atoms per core (thread) is a system in the normal GROMACS scaling regime. 16 OMP threads is more than is useful on other HPC systems, but since we don't know what your hardware is, whether you are investigating something useful is your decision. The crash mentions the calc_cell_indices function (see below). Is this somehow a problem with memory not being sufficient at the MPI interface at this function? I'm not sure how to proceed further. Any help would be greatly appreciated. If there is a problem with GROMACS (which so far I doubt), we'd need a stack trace that shows a line number (rather than addresses) in order to start to locate it. Mark Gromacs version is 4.6.3. Thank you very much for your time. James On 4 September 2013 16:05, Mark Abraham mark.j.abra...@gmail.com wrote: On Sep 4, 2013 7:59 AM, James jamesresearch...@gmail.com wrote: Dear all, I'm trying to run Gromacs on a Fujitsu supercomputer but the software is crashing. I run grompp: grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top and it produces the error: jwe1050i-w The hardware barrier couldn't be used and continues processing using the software barrier. taken to (standard) corrective action, execution continuing. error summary (Fortran) error number error level error count jwe1050i w 1 total error count = 1 but still outputs topol.tpr so I can continue. There's no value in compiling grompp with MPI or in double precision. I then run with export FLIB_FASTOMP=FALSE source /home/username/Gromacs463/bin/GMXRC.bash mpiexec mdrun_mpi_d -ntomp 16 -v but it crashes: starting mdrun 'testrun' 5 steps, 100.0 ps. jwe0019i-u The program was terminated abnormally with signal number SIGSEGV. signal identifier = SEGV_MAPERR, address not mapped to object error occurs at calc_cell_indices._OMP_1 loc 00233474 offset 03b4 calc_cell_indices._OMP_1 at loc 002330c0 called from loc 02088fa0 in start_thread start_thread at loc 02088e4c called from loc 029d19b4 in __thread_start __thread_start at loc 029d1988 called from o.s. error summary (Fortran) error number error level error count jwe0019i
Re: [gmx-users] problem in NPT equilibration step
http://www.gromacs.org/Documentation/Terminology/Pressure_Coupling and http://www.gromacs.org/Documentation/Terminology/Pressure are useful here. Mark On Mon, Oct 14, 2013 at 4:32 PM, srinathchowdary srinathchowd...@gmail.comwrote: The barostat tries to equilibrate the system at the desired pressure, there will be fluctuations and these fluctuations are little higher for Parrinello-rahman if started far away from equilibrium value. I would suggest to start from berendsen and then extend it to P-R. Also, you should run little longer time for the system to reach equilibrium regards sri On Mon, Oct 14, 2013 at 9:13 AM, Preeti Choudhary preetichoudhary18111...@gmail.com wrote: Dear Gromacs user, I am trying to simulate a protein (nmr structure).I have successfully done energy minimisation step.Also I have equilibrated the system a 298 k (which is achieved from 100 ps run) .Now,I am trying to equilibrate the system at 1 bar pressure.After a run of 100 ps ,I am getting average pressure of the system as 4.9 bar.Then I extended this simulation for 50 ps(total 150 ps from start) ,so the av. pressure dropped to 1.5 bar.Then,I again extended this simulation for further 50 ps(Total 200 ps from start),pressure raised to 2.14 bar.Again ,I extended this simulation for further 50 ps(Total 250 ps),pressure raised to 3.56 bar.Similarly,it av. pressure is 2.98 bar,2.85 bar,2.41 bar for 300ps, 350 ps and 400 ps.I am not able to equilibrate the system at 1 bar pressure.What should be done in these cases? I am using opls-aa force field,tip-4 water model,for pressure coupling I am using following parameters: ; Pressure coupling is on pcoupl= Parrinello-Rahman; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 refcoord_scaling = com note :the initial pressure at the beginning of npt simulation and at the end of nvt simuation is -311.41 bar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- V.Srinath Chowdary -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] recalculating .trr from .xtc
Also, the precision was selected when the xtc file was written, ie in the mdp file. Mark On Oct 15, 2013 3:24 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/14/13 7:56 PM, Leandro Bortot wrote: Dear GROMACS users, Does anyone know how significant is the difference between the original .trr file from a simulation and a recalculated .trr from a whole system .xtc (mdrun -rerun traj.xtc -o traj.trr)? I mean... do you know how big would be the error induced by this recalculation procedure? I'm not interested in calculating autocorrelation functions. Most of my analysis are related to the atom positions over time and free energy calculations. Position-related quantities should be impacted very little. Given that you can't acquire precision though, I see no point in even generating a .trr file - the .xtc has the same information while occupying less disk space. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy drift - comparison of double and single precision
On Sat, Oct 12, 2013 at 11:07 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: 2013/10/12 Mark Abraham mark.j.abra...@gmail.com Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Do you suggest that SETTLE is the cause of the drift? Seems likely to me, but I would certainly try to compare apples with apples before reaching that conclusion! (note: If I did not mistaken, my drift would be 0.18 [k_B T / ns / atom], quite close of the figures shown in their figure 2.) Your log file has 51000 atoms (most of which are presumably water), so 4500/10/51000 is 0.0088 kJ/mol/ns/atom. In their Figure 2, they show a drift for single and double precision, and it is not the case for my double precision simulation, so maybe SETTLE is no the cause of my trouble? There are many differences in the simulations (you have protein, Fig 2 uses 2fs time steps, PME settings are different), so there is not yet any basis for assigning the reason for differences in drift. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the If I remember well, their demonstration was true whatever the integrator. Nevertheless, I also tested the leap-frog integrator, and I observe the same drift in energy. So maybe their explanation is still applicable. The authors of that paper show Desmond's drift with RATTLE (an iterative solver), not SETTLE (a constant-time analytical solver). Desmond's drift with SETTLE would have been interesting to see. A cost/benefit analysis of simulation wall-clock time vs errors in the simulation observables for the different solvers would also be interesting. Projecting the total drift from my estimate above back onto Fig 1 of their paper is instructive ;-) .log files might be informative. Here is the link where you can find the log file: http://dx.doi.org/10.6084/m9.figshare.821211 The compiler traveled on the Ark, and the binary was compiled for a machine less capable than the SSE4.1 machine you ran it on. Perhaps the compiler is correct (there are certainly known bugs in *later* gcc minor releases; get the latest), but even if the compiler is correct, you will probably observe things go faster if you fix those ;-) Mark Thanks for your comments! Guillaume Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can
Re: [gmx-users] DSSP installation on Ubuntu 12.10
Maintaining your login scripts is a basic UNIX issue, not a GROMACS issue. Google knows a lot more about it than anybody here ;-) Mark On Fri, Oct 11, 2013 at 2:57 PM, Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs user, Can anyone tell me how to arrange for my login scripts to source gromacs automatically? Justin just point that to me and in Gromacs website it is written search the web for that, anyone know how to do that? Thanks On Saturday, October 12, 2013 1:12 AM, Mass masstransfer_2...@yahoo.com wrote: Hi Justin, Sorry for the mistake, I typed in terminal do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump and got the following error, Program do_dssp, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: bLac_orig_md2.trr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I can see the file bLac_orig_md2.trr in the directory any comments? On Saturday, October 12, 2013 12:55 AM, Justin Lemkul jalem...@vt.edu wrote: On 10/11/13 1:34 AM, Mass wrote: Dear Mark, Thanks for your comments, I uninstalled my previous Gromacs version ( from Ubuntu software centre I just removed it) . and followed the dirty and quick installation on Gromacs website tar xfz gromacs-4.6.3.tar.gz cd gromacs-4.6.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON make sudo make install source /usr/local/gromacs/bin/GMXRC I have one question here, why when I run mdrun in my home directory it is telling me that Gromacs is not installed, but when I source it again and go to my home directory after that mdrun show Gromacs version-4.6.3. any comments on this? how can I call gromacs without sourcing every time Configure your login scripts to do it for you. secondly when I do do_dssp do_dssp -f bLac_orig_md2.trr -s bLac_orig_md2.tpr -sc Secondary_Structure_analysis_original_dss.xvg -ssdump I am getting following error Program mdrun, VERSION 4.6.3 Source code file: /home/mass/gromacs-4.6.3/src/gmxlib/gmxfio.c, line: 524 Can not open file: topol.tpr For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Whatever you typed above is not what you typed in the terminal (always copy and paste!), because do_dssp is looking for topol.tpr, which is the default name for -s. If you do not specify a particular required input, all Gromacs programs look for default names. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy drift - comparison of double and single precision
On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy drift - comparison of double and single precision
Didn't see any problem in the .mdp. -4500 kJ/mol in 10ns over (guessing) 30K atoms is 0.015 kJ/mol/ns/atom. k_B T is at least 100 times larger than that. I bet the rest of the lysozyme model physics is not accurate to less than 1% ;-) There are some comparative numbers at http://dx.doi.org/10.1016/j.cpc.2013.06.003 - the two systems are rather different but they share the use of SETTLE. Note that using md-vv guarantees the 2007 paper is inapplicable, because GROMACS did not have a velocity Verlet integrator back then. Sharing the .log files might be informative. Mark On Fri, Oct 11, 2013 at 11:38 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi, sorry for my last post! I re-write my e-mail (with some additional information) and I provide the links to my files ;-) I compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision / Gromacs 4.6.3 lysozyme in water / NVE ensemble / double precision / Gromacs 4.6.3 ... and what I found was quite ... disturbing (see the plots of the total energy: http://dx.doi.org/10.6084/m9.figshare.820153). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! Here is the link to the ‘mdout.mdp’ file (http://dx.doi.org/10.6084/m9.figshare.820154) so you can check what mdp options I used. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 2013/10/11 Mark Abraham mark.j.abra...@gmail.com On Oct 11, 2013 7:59 PM, Guillaume Chevrot guillaume.chev...@gmail.com wrote: Hi all, I recently compared the total energy of 2 simulations: lysozyme in water / NVE ensemble / single precision lysozyme in water / NVE ensemble / double precision ... and what I found was quite ... disturbing (see the attached figure - plots of the total energy). I observe a constant drift in energy in the case of the single precision simulation. Did I do something wrong*? Any remarks are welcomed! I join the ‘mdout.mdp’ file so you can check what mdp options I used. Maybe. Unfortunately we cannot configure the mailing list to allow people to send attachments to thousands of people, so you will need to do something like provide links to files on a sharing service. My second question is: if I did not do something wrong, what are the consequences on the simulation? Can I trust the results of single precision simulations? Yes, as you have no doubt read in the papers published by the GROMACS team. Regards, Guillaume *PS: I am not the only one encountering this behavior. In the literature, this problem has already been mentioned: http://jcp.aip.org/resource/1/jcpsa6/v126/i4/p046101_s1 ... which is six years old, examining the properties of code seven years old. Life has moved on! :-) Even if you have found a problem, it is a big assumption that this is (still) the cause. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] DSSP installation on Ubuntu 12.10
Hi, Since the release of 4.5.5, DSSP totally changed its command-line interface. So old GROMACS code cannot work with new DSSP. You need to get the old version of DSSP to use with old GROMACS, or new GROMACS code to work with either DSSP. Mark On Thu, Oct 10, 2013 at 1:37 PM, Mass masstransfer_2...@yahoo.com wrote: Dear Gromacs users, I have asked this questions before and Justin gave some answers which I could solve my problem based on his answer. I am using Ubuntu 12.10 and installed gromacs 4.5.5-2. this is what I have done 2- I moved this file to usr/local/bin 1- first I downloaded the dssp wget ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4-linux-amd64-O~/dssp 2- I moved this file to usr/local/bin then I run do_dssp and I was asked to select a group Select a group: 1 Selected 1: 'Protein' There are 162 residues in your selected group trn version: GMX_trn_file (single precision) Reading frame 0 time0.000 Back Off! I just backed up ddQ0FCUF to ./#ddQ0FCUF.1# after that I am getting Program do_dssp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/tools/do_dssp.c, line: 572 Fatal error: Failed to execute command: /usr/local/bin/dssp -na ddQ0FCUF ddzUlAvc /dev/null 2 /dev/null For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I really appreciate if anyone can tell me simple and step-by step solution (I am a beginner user). Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] CHARMM36 force field available for GROMACS
Great! Many thanks Justin, and the CHARMM team! Mark On Tue, Oct 8, 2013 at 10:16 PM, Justin Lemkul jalem...@vt.edu wrote: All, I am pleased to announce the immediate availability of the latest CHARMM36 force field in GROMACS format. You can obtain the archive from our lab's website at http://mackerell.umaryland.**edu/CHARMM_ff_params.htmlhttp://mackerell.umaryland.edu/CHARMM_ff_params.html . The present version contains up-to-date parameters for proteins, nucleic acids, lipids, some carbohydrates, CGenFF version 2b7, and a variety of of other small molecules. Please refer to forcefield.doc, which contains a list of citations that describe the parameters, as well as the CHARMM force field files that were used to generate the distribution. We have validated the parameters by comparing energies of a wide variety of molecules within CHARMM and GROMACS and have found excellent agreement between the two. If anyone has any issues or questions, please feel free to post them to this list or directly to me at the email address below. Happy simulating! -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installing Extended Genbox
I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at 6:24 AM, Tegar Nurwahyu Wijaya tnurwahyuwij...@gmail.com wrote: Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Installing Extended Genbox
Since that patch is already merged, Tegar can just check out the (default) master branch - see http://www.gromacs.org/Developer_Zone/Git. The CMake build works the same way. I would suggest just using your-build-directory/bin/genbox once you have built it, i.e. do not go to the trouble of installing the development version. You should prefer to use the normal versions of all the tools unless you want to live on the edge! Mark On Tue, Oct 1, 2013 at 5:01 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/1/13 10:58 AM, Tegar Nurwahyu Wijaya wrote: Hi Mark, Thank you for your reply. Actually I am not trying to add it to the repository. I have gromacs 4.6 installed in my computer. When I was trying using genbox, an error occurred caused by memory lacking. After searched this mailing list, I got that extended genbox code that can fix my problem. But I don't know how to put that code into my installed gromacs 4.6. Do you or anybody know how to do that? You need to clone the git repository (i.e. the development code) and then apply the patch with the instructions at the link Mark sent you. Further up on the page is how you get started in terms of obtaining the development code from git. It is unwise to try to apply a patch from the master branch on version 4.6; I doubt it would even work. -Justin Regards, Tegar On Tue, Oct 1, 2013 at 10:12 AM, Mark Abraham mark.j.abra...@gmail.com* *wrote: I would generally not try to add it to an existing source repository. Instead, follow one of the suggestions in http://www.gromacs.org/**Developer_Zone/Git/Gerrit#How_** do_I_get_a_copy_of_my_commit_**for_which_someone_else_has_** uploaded_a_patch.3fhttp://www.gromacs.org/Developer_Zone/Git/Gerrit#How_do_I_get_a_copy_of_my_commit_for_which_someone_else_has_uploaded_a_patch.3f to check out that version. Mark On Tue, Oct 1, 2013 at 6:24 AM, Tegar Nurwahyu Wijaya tnurwahyuwij...@gmail.com wrote: Dear all, I want to install Extended Genbox from gerrit. https://gerrit.gromacs.org/#/**c/1175/https://gerrit.gromacs.org/#/c/1175/ How can I put this code into my existing gromacs installation? Thanks. Regards, Tegar -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/**Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Preprocessor statements
No, there's no way to do that. But you can monitor the output trajectory file yourself, live. Mark On Thu, Sep 26, 2013 at 4:49 PM, Dr. Vitaly Chaban vvcha...@gmail.com wrote: Unlikely possible... But yeah, the feature might be handy. Dr. Vitaly V. Chaban On Thu, Sep 26, 2013 at 4:20 PM, grita cemilyi...@arcor.de wrote: Hi guys, Is it possible to specify in the topol.top file preprocessor statements, so that you can stop the simulation prematurely? I pull two molecules together and I'd like to stop the simulation if the center of mass distance of the molecules is less than xx nm. Best, grita -- View this message in context: http://gromacs.5086.x6.nabble.com/Preprocessor-statements-tp5011469.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] segfault when running the alchemistry.org ethanol solvation free energy tutorial
I found the -multi version of that tutorial a bit temperamental... Michael Shirts suggested that double precision is more reliable for expanded ensemble. Hopefully he can chime in in a day or two. Mark On Thu, Sep 26, 2013 at 9:00 PM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Dear Users: Has anyone successfully run the free energy tutorial at http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Direct_ethanol_solvation_free_energy ? I just tried it and I get a segmentation fault immediately (see output at the end of this post). I get a segfault with both 4.6.3 and 4.6.1. Note that if I modify the .mdp file to set free-energy = no , then the simulation runs just fine. (I have, of course, set init-lambda-state in the .mdp file that I downloaded from the aforementioned site and I get a segfault with any value of init-lambda-state from 0 to 8). gpc-f103n084-$ mdrun -nt 1 -deffnm ethanol.1 -dhdl ethanol.1.dhdl.xvg :-) G R O M A C S (-: GROup of MAchos and Cynical Suckers :-) VERSION 4.6.3 (-: Contributions from Mark Abraham, Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van Buuren, Pär Bjelkmar, Rudi van Drunen, Anton Feenstra, Gerrit Groenhof, Christoph Junghans, Peter Kasson, Carsten Kutzner, Per Larsson, Pieter Meulenhoff, Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz, Michael Shirts, Alfons Sijbers, Peter Tieleman, Berk Hess, David van der Spoel, and Erik Lindahl. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2012,2013, The GROMACS development team at Uppsala University The Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. :-) mdrun (-: Option Filename Type Description -s ethanol.1.tpr InputRun input file: tpr tpb tpa -o ethanol.1.trr Output Full precision trajectory: trr trj cpt -x ethanol.1.xtc Output, Opt. Compressed trajectory (portable xdr format) -cpi ethanol.1.cpt Input, Opt. Checkpoint file -cpo ethanol.1.cpt Output, Opt. Checkpoint file -c ethanol.1.gro Output Structure file: gro g96 pdb etc. -e ethanol.1.edr Output Energy file -g ethanol.1.log Output Log file -dhdl ethanol.1.dhdl.xvg Output, Opt! xvgr/xmgr file -field ethanol.1.xvg Output, Opt. xvgr/xmgr file -table ethanol.1.xvg Input, Opt. xvgr/xmgr file -tabletf ethanol.1.xvg Input, Opt. xvgr/xmgr file -tablep ethanol.1.xvg Input, Opt. xvgr/xmgr file -tableb ethanol.1.xvg Input, Opt. xvgr/xmgr file -rerun ethanol.1.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt -tpi ethanol.1.xvg Output, Opt. xvgr/xmgr file -tpid ethanol.1.xvg Output, Opt. xvgr/xmgr file -ei ethanol.1.edi Input, Opt. ED sampling input -eo ethanol.1.xvg Output, Opt. xvgr/xmgr file -j ethanol.1.gct Input, Opt. General coupling stuff -jo ethanol.1.gct Output, Opt. General coupling stuff -ffout ethanol.1.xvg Output, Opt. xvgr/xmgr file -devout ethanol.1.xvg Output, Opt. xvgr/xmgr file -runav ethanol.1.xvg Output, Opt. xvgr/xmgr file -px ethanol.1.xvg Output, Opt. xvgr/xmgr file -pf ethanol.1.xvg Output, Opt. xvgr/xmgr file -ro ethanol.1.xvg Output, Opt. xvgr/xmgr file -ra ethanol.1.log Output, Opt. Log file -rs ethanol.1.log Output, Opt. Log file -rt ethanol.1.log Output, Opt. Log file -mtx ethanol.1.mtx Output, Opt. Hessian matrix -dn ethanol.1.ndx Output, Opt. Index file -multidir ethanol.1 Input, Opt., Mult. Run directory -membed ethanol.1.dat Input, Opt. Generic data file -mp ethanol.1.top Input, Opt. Topology file -mn ethanol.1.ndx Input, Opt. Index file Option Type Value Description -- -[no]h bool no Print help info and quit -[no]version bool no Print version info and quit -niceint0 Set the nicelevel -deffnm string ethanol.1 Set the default filename for all file options -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]pd bool no Use particle decompostion -dd vector 0 0 0 Domain decomposition grid, 0 is optimize -ddorder enum interleave DD node order: interleave, pp_pme or cartesian -npmeint-1 Number of separate nodes to be used for PME, -1
Re: [gmx-users] Re: grompp for minimization: note warning
If diff says there are no changes, then you're not comparing with the file you changed... On Sep 25, 2013 1:59 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear Mark The UNIX tool diff is your friend for comparing files. Thanks for your suggestion. I used diff and sdiff toll for comparing 2 files (before and after correction). diff old.gro new.gro These tolls did not give me any output file or text containing difference between 2 files. In this condition, how should I find difference between 2 gro files? Best wishes for you -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] OPLS/AA + TIP5P, anybody?
You should be able to minimize with CG and TIP5P by eliminating constraints, by making the water use a flexible molecule, e.g. define = -DFLEXIBLE (or something). Check your water .itp file for how to do it. Mark On Tue, Sep 24, 2013 at 10:25 PM, gigo g...@ibb.waw.pl wrote: Dear GMXers, Since I am interested in interactions of lone electron pairs of water oxygen within the active site of an enzyme that I work on, I decided to give TIP5P a shot. I use OPLSAA. I run into troubles very fast trying to minimize freshly solvated system. I found on the gmx-users (http://lists.gromacs.org/pipermail/gmx-users/2008-March/032732.html) that cg and constraints don't go together when TIP5P is to be used - thats OK. It turned out, however, that I was not able to minimize my protein even with steepest descent. The system minimizes with TIP4P pretty well (emtol=1.0). In the meantime I tried to minimize short peptide - 10aa, did not work as well. What happens? The LP of water used to get too close to positively charged hydrogens (without VDW radius) on arginine. It looks like this: Step= 579, Dmax= 8.0e-03 nm, Epot= -1.40714e+05 Fmax= 1.20925e+04, atom= 171 Step= 580, Dmax= 9.6e-03 nm, Epot= -1.41193e+05 Fmax= 8.13923e+04, atom= 171 Step= 581, Dmax= 1.1e-02 nm, Epot= -1.43034e+05 Fmax= 1.03648e+06, atom= 11181 Step= 585, Dmax= 1.7e-03 nm, Epot= -1.46878e+05 Fmax= 4.23958e+06, atom= 11181 Step= 587, Dmax= 1.0e-03 nm, Epot= -1.49565e+05 Fmax= 9.43285e+06, atom= 11181 Step= 589, Dmax= 6.2e-04 nm, Epot= -1.59042e+05 Fmax= 3.55920e+07, atom= 11181 Step= 591, Dmax= 3.7e-04 nm, Epot= -1.69054e+05 Fmax= 7.79944e+07, atom= 11181 Step= 593, Dmax= 2.2e-04 nm, Epot= -1.85575e+05 Fmax= 2.27640e+08, atom= 11181 Step= 595, Dmax= 1.3e-04 nm, Epot= -2.35034e+05 Fmax= 5.88938e+08, atom= 17181 Step= 597, Dmax= 8.0e-05 nm, Epot= -2.39154e+05 Fmax= 1.22615e+09, atom= 11181 Step= 598, Dmax= 9.6e-05 nm, Epot= -2.67157e+05 Fmax= 1.96782e+09, atom= 11181 Step= 600, Dmax= 5.8e-05 nm, Epot= -4.37260e+05 Fmax= 1.08988e+10, atom= 11181 Step= 602, Dmax= 3.5e-05 nm, Epot= -4.65654e+05 Fmax= 1.29609e+10, atom= 11181 Step= 604, Dmax= 2.1e-05 nm, Epot= -1.17945e+06 Fmax= 1.31028e+11, atom= 11181 Step= 607, Dmax= 6.3e-06 nm, Epot= -3.07551e+06 Fmax= 6.04297e+11, atom= 11181 Step= 610, Dmax= 1.9e-06 nm, Epot= -4.26709e+06 Fmax= 1.61390e+12, atom= 11181 Step= 611, Dmax= 2.3e-06 nm, Epot= -4.39724e+06 Fmax= 2.14416e+12, atom= 11181 Step= 613, Dmax= 1.4e-06 nm, Epot= -1.27489e+07 Fmax= 1.03223e+13, atom= 17181 Step= 614, Dmax= 1.6e-06 nm, Epot= -5.23118e+06 Fmax= 3.18465e+12, atom= 11181 Energy minimization has stopped, but the forces havenot converged to the (...) In this example atom 171 is HH21 of ARG, and 11181 is oxygen of water that got close to this ARG. Sometimes the epot turns nan at the end. If you would like to reproduce, I put the peptide.pdb, the mdp file and the running script at http://shroom.ibb.waw.pl/tip5p . If anybody have any suggestions how to minimize (deep) with OPLSAA + TIP5P in gromacs (4.6.3 preferably...) without constraining bond lengths (which is also problematic), I will be very very grateful. Best, Grzegorz Wieczorek -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] SPC with amber?
The FF+water combinations still work the same way they did 3 years ago! :-) The important question is whether validation for the observables has occurred. (And no relevant problems were seen). If the paper does not support its decision to mix and match, go and ask them why it was reasonable! Mark On Tue, Sep 24, 2013 at 10:58 PM, Rafael I. Silverman y de la Vega rsilv...@ucsc.edu wrote: Dear all, I have been trying to evaluate a paper that used amber99 with SPC water to simulate a protein. How would this affect the results, is it important? I googled for a bit, all I found was: Amber, charmm and OPLS-AA were developed with TIP3P, and that should be the default. Except that charmm uses a TIP3P with lennard-Jones on the waters, and that should probably be the default with charmm. B.t.w., how transferable are water models between ff's? I've always been thought that they are actually non-transferable (or at least that is what I remember), making e.g. Amber/SPCe a bad option, as would gromos/tip4p.? Nobody really knows. from 2010, have things changed in 3 years, and forcefields work better with water models not developed specifically for that ff? Thanks -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Funky output trajectory (lines all over the place)
On Sep 23, 2013 9:23 AM, Jonathan Saboury jsab...@gmail.com wrote: I tried minimizing a box of cyclohexanes and water. The first frame is fine, but after that seemingly random lines form in vmd with the cyclohexanes. The waters seem to minimizing just fine though. I am sure I am just doing something extremely silly and I just don't know it because of ignorance. I have no formal training on simulations, you are my only hope! Google is pretty useful, too ;-) http://www.gromacs.org/Documentation/FAQsdeals with this kind of issue. Mark Perhaps using the em.gro with the em.trr is not the correct way to visualize? I used the command: vmd em.gro em.trr Or something is wrong with my em.mdp? em.mdp: http://pastebin.com/raw.php?i=LPPN5xRF Commands used: http://pastebin.com/raw.php?i=Jk0fKLJj Here are all the files, in case you need them: http://www.sendspace.com/file/gx8j97 Sorry for dumping all of this, but I am genuinely stuck. I've tried reading about the mdp file format but i only understand ~5%. If I could have done more I would have tried :/ Thank you all, it is really appreciated. -Jonathan Saboury -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] energy minimization
On Sep 23, 2013 9:08 AM, marzieh dehghan dehghanmarz...@gmail.com wrote: Hi every body in order to protein- ligand docking, energy minimization was done by GROMACS. I did the following steps for insulin pdb file: 1- pdb2gmx -ignh -f 3inc.pdb -o test.pdb -p topol.top -water spce 2- grompp -f em.mdp -c test.pdb -p topol.top -o em.tpr 3-mdrun -v -deffnm em 4- editconf -f em.gro -o final.pdb -c -d 1.0 -bt cubic everything was perfect, but the final pdb file has two problems: 1- chain ID was missed. 2- insulin contains two chains (A B) which connect by disulfide bond, but after energy minimization, two chains are separated. Did pdb2gmx even report it being made? Mark I would like to know how to solve these problems? best regards -- *Marzieh Dehghan PhD Candidate of Biochemistry Institute of biochemistry and Biophysics (IBB) University of Tehran, Tehran- Iran.* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] The charge of cofactor and ligand
How do GAFF and acpype work? Mark On Mon, Sep 23, 2013 at 5:47 PM, aixintiankong aixintiank...@126.com wrote: Dear prof, can i use the RESP charge for the cofactor NAD+ and AM1-BBC charge for ligand and then use acpype to generate GAFF force field parameter for the NAD+ and ligand? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] confusion about implicint solvent
On Mon, Sep 23, 2013 at 8:08 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: Hi, Admittedly, both the documentation on these features and the communication on the known issues with these aspects of GROMACS has been lacking. Here's a brief summary/explanation: - GROMACS 4.5: implicit solvent simulations possible using mdrun-gpu which is essentially mdrun + OpenMM, hence it has some limitations, most notably it can only run on a single GPU. The performance, depending on setting, can be up to 10x higher than on the CPU. - GROMACS 4.6: the native GPU acceleration does supports only explicit solvent, mdrun + OpenMM is still available (exactly for implicit solvent runs), but has been moved to the contrib section which means that it is not fully supported. Moreover, OpenMM support - unless somebody volunteers for maintenance of the mdrun-OpenMM interface - will be dropped in the next release. I can't comment much on the implicit solvent code on the CPU side other than the fact that there have been issues which AFAIK limit the parallelization to a rather small number of cores, hence the achievable performance is also limited. I hope others can clarify this aspect. IIRC the best 4.5 performance for CPU-only implicit solvent used infinite cut-offs and SIMD acceleration. The SIMD is certainly broken in 4.6 (and IIRC was explicitly disabled at some point after 4.6.3). There is limited enthusiasm for fixing things (e.g. see parts of http://redmine.gromacs.org/issues/1292) but nobody with the skills has so far applied the time to do so. As always with an open-source project, if you want something, be prepared to roll up your sleeves and work, or hit your knees and pray! :-) Mark Cheers, -- Szilárd On Mon, Sep 23, 2013 at 7:34 PM, Francesco frac...@myopera.com wrote: Good afternoon everybody, I'm a bit confuse about gromacs performances with implicit solvent. I'm simulating a 1000 residues protein with explicit solvent, using both a cpu and a gpu cluster. With a gpu node (12 cores and 3 M2090 gpu ) I reach 10 ns/day, while with no gpu and 144 cores I got 34 ns/day. Because I have several mutants (more than 50) I have to reduce the average simulation time and I was considering different option such as the use of implicit solvent. I tried with both the clusters and using gromacs 4.6 and 4.5 but the performances are terrible (1 day for 100ps) comparing to the explicit solvent. I read all the other messages on the mailing-list and the documentation, but the mix of old and new features/posts really confuses me a lot. Here (http://www.gromacs.org/Documentation/Acceleration_and_parallelization) it is said that with the gpu 4.5 and implicit solvent I should expect a substantial speedup. Here ( http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM#Benchmark_results.3a_GROMACS_CPU_vs_GPU ) I found this sentence It is ultimately up to you as a user to decide what simulations setups to use, but we would like to emphasize the simply amazing implicit solvent performance provided by GPUs. I follow the advise found in the mailing list and read both the documentation (site and manual), but I can't figured it out what should I do. How can you guys have amazing performances? I also found this answer from a last March post (http://gromacs.5086.x6.nabble.com/Implicit-solvent-MD-is-not-fast-and-not-accurate-td5006659.html#none) that confuses me even more. Performance issues are known. There are plans to implement the implicit solvent code for GPU and perhaps allow for better parallelization, but I don't know what the status of all that is. As it stands (and as I have said before on this list and to the developers privately), the implicit code is largely unproductive because the performance is terrible. Should I skip the idea of using implicit solvent and try something else? these are a set of parameters that I used (also the -pd flag) ; Run parameters integrator = sd tinit = 0 nsteps = 5 dt= 0.002 ; Output control nstxout = 5000 nstvout = 5000 nstlog = 5000 nstenergy = 5000 nstxtcout= 5000 xtc_precision = 1000 energygrps = system ; Bond parameters continuation= no constraints = all-bonds constraint_algorithm = lincs lincs_iter = 1 lincs_order = 4 lincs_warnangle = 30 ; Neighborsearching ns_type = simple nstlist = 0 rlist= 0 rcoulomb= 0 rvdw = 0 ; Electrostatics coulombtype = cut-off pbc= no comm_mode= Angular implicit_solvent = GBSA gb_algorithm = OBC nstgbradii = 1.0 rgbradii = 0 gb_epsilon_solvent= 80 gb_dielectric_offset= 0.009
Re: [gmx-users] restarting the crashed run
No, because then the state.cpt file would be redundant :-) All you can do re-start from the beginning, because the .tpr file only has the initial state. You can extend the number of steps, but you can't magically produce the state after the first simulation just from the initial one. (If you can, you'll be hugely popular here, though!) Mark On Sun, Sep 22, 2013 at 12:03 PM, Nidhi Katyal nidhikatyal1...@gmail.com wrote: Thank you Justin for your reply. Pt 3 should be the correct way to proceed. But somehow if I have lost my state.cpt file, can I continue my run using following commands: tpbconv -s previous.tpr -extend timetoextendby -o next.tpr mdrun -v -s next.tpr -o next.trr -c next.gro -g next.log -e next.ene -noappend trjcat -f previous.trr next.trr -o combine.trr On Sun, Sep 22, 2013 at 1:43 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/21/13 3:46 PM, Nidhi Katyal wrote: Dear all I would like to know the difference between restarting our crashed runs by 1) first generating next.tpr using tpbconv -extend option then running grompp with this *.tpr file Why would you run grompp? If you're using it as a source of coordinates, you're going to be dealing with the initial state, not the last state of the previous simulation, so that's garbage. If you're restarting a crash, then presumably there is no need at all to invoke tpbconv or grompp. and finally running mdrun but with no cpi option Makes no sense. You're basically obliterating the previous simulation. 2) same as 1 but with -cpi option Still no need for grompp, but if providing -cpi to mdrun, you're resuming from the correct state. 3) using only mdrun command with cpi option and with previous *.tpr (ie not creating new tpr by tpbconv option) This is the correct way to proceed. The run will pick up from the state stored in the .cpt file and proceed with the number of steps originally specified in the .tpr file. 4) using procedure 3 but with no state.cpt file The run should start over. Secondly, if state.cpt contains all the information to continue the simulation then why the simulation should continue at all without providing these files as in procedure 1 and 4 Without a .cpt file, the run starts over from the beginning. -Justin -- ==** Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalemkul@outerbanks.umaryland.**edu jalem...@outerbanks.umaryland.edu | (410) 706-7441 ==** -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Minimum distance periodic images, protein simulation
You can try a run in implicit solvent to get a feel for the maximum diameter of the protein while unfolding. You will not have any certainty unless you can afford a box whose diameter is that of the straight-line peptide... Mark On Sat, Sep 21, 2013 at 1:03 PM, aksharma arunsharma_...@yahoo.com wrote: Hi Justin, Thanks for your reply. I have some follow-up questions. Since the simulation is high temperature (450 K) there is slight unfolding of the protein. The box was set up as rhombic dodecahedron with 1.2 nm as the distance between solute and edge of box. pdb2gmx -f 1L2Y.pdb -o 1L2Y-processed.gro -ignh -water spce The cutoffs are 0.9 nm for VDW and electrostatics. Do you suggest using an even bigger box for studying unfolding? Or is there something else that could be going on? Do you have any ball park suggestions for a good size of the box or is this something that I would have to experiment with different sizes until I land a suitable box. Thanks a lot, -- View this message in context: http://gromacs.5086.x6.nabble.com/Minimum-distance-periodic-images-protein-simulation-tp5011343p5011347.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)
On Sat, Sep 21, 2013 at 2:45 PM, James jamesresearch...@gmail.com wrote: Dear Mark and the rest of the Gromacs team, Thanks a lot for your response. I have been trying to isolate the problem and have also been in discussion with the support staff. They suggested it may be a bug in the gromacs code, and I have tried to isolate the problem more precisely. First, do the GROMACS regression tests for Verlet kernels pass? (Run them all, but those with nbnxn prefix are of interest here.) They likely won't scale to 16 OMP threads, but you can vary OMP_NUM_THREADS environment variable to see what you can see. Considering that the calculation is run under MPI with 16 OpenMP cores per MPI node, the error seems to occur under the following conditions: A few thousand atoms: 1 or 2 MPI nodes: OK Double the number of atoms (~15,000): 1 MPI node: OK, 2 MPI nodes: SIGSEGV error described below. So it seems that the error occurs for relatively large systems which use MPI. ~500 atoms per core (thread) is a system in the normal GROMACS scaling regime. 16 OMP threads is more than is useful on other HPC systems, but since we don't know what your hardware is, whether you are investigating something useful is your decision. The crash mentions the calc_cell_indices function (see below). Is this somehow a problem with memory not being sufficient at the MPI interface at this function? I'm not sure how to proceed further. Any help would be greatly appreciated. If there is a problem with GROMACS (which so far I doubt), we'd need a stack trace that shows a line number (rather than addresses) in order to start to locate it. Mark Gromacs version is 4.6.3. Thank you very much for your time. James On 4 September 2013 16:05, Mark Abraham mark.j.abra...@gmail.com wrote: On Sep 4, 2013 7:59 AM, James jamesresearch...@gmail.com wrote: Dear all, I'm trying to run Gromacs on a Fujitsu supercomputer but the software is crashing. I run grompp: grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top and it produces the error: jwe1050i-w The hardware barrier couldn't be used and continues processing using the software barrier. taken to (standard) corrective action, execution continuing. error summary (Fortran) error number error level error count jwe1050i w 1 total error count = 1 but still outputs topol.tpr so I can continue. There's no value in compiling grompp with MPI or in double precision. I then run with export FLIB_FASTOMP=FALSE source /home/username/Gromacs463/bin/GMXRC.bash mpiexec mdrun_mpi_d -ntomp 16 -v but it crashes: starting mdrun 'testrun' 5 steps, 100.0 ps. jwe0019i-u The program was terminated abnormally with signal number SIGSEGV. signal identifier = SEGV_MAPERR, address not mapped to object error occurs at calc_cell_indices._OMP_1 loc 00233474 offset 03b4 calc_cell_indices._OMP_1 at loc 002330c0 called from loc 02088fa0 in start_thread start_thread at loc 02088e4c called from loc 029d19b4 in __thread_start __thread_start at loc 029d1988 called from o.s. error summary (Fortran) error number error level error count jwe0019i u 1 jwe1050i w 1 total error count = 2 [ERR.] PLE 0014 plexec The process terminated abnormally.(rank=1)(nid=0x03060006)(exitstatus=240)(CODE=2002,1966080,61440) [ERR.] PLE The program that the user specified may be illegal or inaccessible on the node.(nid=0x03060006) Any ideas what could be wrong? It works on my local intel machine. Looks like it wasn't compiled correctly for the target machine. What was the cmake command, what does mdrun -version output? Also, if this is the K computer, probably we can't help, because the compiler docs are officially unavailable to us. National secret, and all ;-) Mark Thanks in advance, James -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use
Re: [gmx-users] No such moleculetype SOL
On Sat, Sep 21, 2013 at 9:06 PM, Jonathan Saboury jsab...@gmail.com wrote: I am doing this tutorial: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html I have set up the randomly placed cyclohexane and water throughout the box. The problem is when i try the command grompp -f em.mdp -c biphase.gro -p cyclohexane.top -o em.tpr it errors telling me No such moleculetype SOL. I know SOL is water, and the .top file does not include any sort of .itp that includes water. Have a look at how Justin's tutorial's .top gets access to a water topology. Mark I've tried to add #include amber99sb.ff/forcefield.itp with no avail. This is strictly just cyclohexane and water, I am not interested in putting a protein inside of it. Commands used: http://pastebin.com/raw.php?i=RaKNCpi4 Files: http://www.sendspace.com/file/ibwk3l Thank you, the help you guys give is extremely appreciated :) -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] MPI runs on a local computer
On Thu, Sep 19, 2013 at 2:48 PM, Xu, Jianqing x...@medimmune.com wrote: Dear all, I am learning the parallelization issues from the instructions on Gromacs website. I guess I got a rough understanding of MPI, thread-MPI, OpenMP. But I hope to get some advice about a correct way to run jobs. Say I have a local desktop having 16 cores. If I just want to run jobs on one computer or a single node (but multiple cores), I understand that I don't have to install and use OpenMPI, as Gromacs has its own thread-MPI included already and it should be good enough to run jobs on one machine. However, for some reasons, OpenMPI has already been installed on my machine, and I compiled Gromacs with it by using the flag: -DGMX_MPI=ON. My questions are: 1. Can I still use this executable (mdrun_mpi, built with OpenMPI library) to run multi-core jobs on my local desktop? Yes Or the default Thread-MPI is actually a better option for a single computer or single node (but multi-cores) for whatever reasons? Yes - lower overhead. 2. Assuming I can still use this executable, let's say I want to use half of the cores (8 cores) on my machine to run a job, mpirun -np 8 mdrun_mpi -v -deffnm md a). Since I am not using all the cores, do I still need to lock the physical cores to use for better performance? Something like -nt for Thread-MPI? Or it is not necessary? You will see improved performance if you set the thread affinity. There is no advantage in allowing the threads to move. b). For running jobs on a local desktop, or single node having ... say 16 cores, or even 64 cores, should I turn off the separate PME nodes (-npme 0)? Or it is better to leave as is? Depends, but usually best to use separate PME nodes. Try g_tune_pme, as Carsten suggests. 3. If I want to run two different projects on my local desktop, say one project takes 8 cores, the other takes 4 cores (assuming I have enough memory), I just submit the jobs twice on my desktop: nohup mpirun -np 8 mdrun_mpi -v -deffnm md1 log1 nohup mpirun -np 4 mdrun_mpi -v -deffnm md2 log2 Will this be acceptable ? Will two jobs be competing the resource and eventually affect the performance? Depends how many cores you have. If you want to share a node between mdruns, you should specify how many (real- or thread-) MPI ranks for each run, and how many OpenMP threads per rank, arrange for one thread per core, and use mdrun -pin and mdrun -pinoffset suitably. You should expect near linear scaling of each job when you are doing it right - but learn the behaviour of running one job per node first! Mark Sorry for so many detailed questions, but your help on this will be highly appreciated! Thanks a lot, Jianqing To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: grompp for minimization: note warning
The UNIX tool diff is your friend for comparing files. On Fri, Sep 20, 2013 at 1:53 PM, shahab shariati shahab.shari...@gmail.com wrote: Dear Tsjerk Thanks for your reply Before correcting the gro file, I knew that gro file is fixed format. I did this correction very carefully. Part of the gro file before and after correction is as follows: - before: - 14DOPCN4 755 0.260 1.726 6.354 14DOPCC5 756 0.263 1.741 6.204 14DOPCC1 757 0.136 1.777 6.423 14DOPCC2 758 0.279 1.580 6.384 14DOPCC3 759 0.383 1.799 6.403 14DOPCC6 760 0.386 1.685 6.132 14DOPCP8 761 0.628 1.683 6.064 14DOPC OM9 762 0.640 1.548 6.123 14DOPC OM10 763 0.747 1.771 6.072 14DOPC OS7 764 0.511 1.755 6.145 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C34 772 0.490 2.037 5.777 14DOPC OS35 773 0.541 2.029 5.644 14DOPC C36 774 0.591 2.142 5.593 14DOPC O37 775 0.595 2.252 5.646 14DOPC C38 776 0.674 2.092 5.476 14DOPC C18 777 -0.004 1.897 5.786 14DOPC C19 778 -0.138 1.837 5.744 14DOPC C20 779 -0.147 1.817 5.593 14DOPC C21 780 -0.196 1.678 5.552 14DOPC C22 781 -0.181 1.637 5.406 14DOPC C23 782 -0.252 1.722 5.301 14DOPC C24 783 -0.241 1.664 5.163 14DOPC C25 784 -0.267 1.738 5.054 14DOPC C26 785 -0.312 1.881 5.044 14DOPC C27 786 -0.368 1.918 4.907 14DOPC C28 787 -0.266 1.941 4.795 14DOPC C29 788 -0.324 2.015 4.674 14DOPC C30 789 -0.377 1.920 4.567 14DOPC C31 790 -0.377 1.984 4.428 14DOPC C32 791 -0.439 1.894 4.321 14DOPC C33 792 -0.358 1.890 4.191 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797 1.136 1.965 5.202 14DOPC C44 798 1.261 1.897 5.146 14DOPC C45 799 1.314 1.786 5.232 14DOPC C46 800 1.319 1.658 5.194 14DOPC C47 801 1.274 1.602 5.062 14DOPC C48 802 1.316 1.457 5.038 14DOPC C49 803 1.266 1.407 4.902 14DOPC C50 804 1.338 1.469 4.782 14DOPC C51 805 1.307 1.406 4.646 14DOPC C52 806 1.160 1.394 4.607 14DOPC C53 807 1.119 1.442 4.468 14DOPC C54 808 0.980 1.407 4.414 - after: - 14DOPCC1 755 0.136 1.777 6.423 14DOPCC2 756 0.279 1.580 6.384 14DOPCC3 757 0.383 1.799 6.403 14DOPCN4 758 0.260 1.726 6.354 14DOPCC5 759 0.263 1.741 6.204 14DOPCC6 760 0.386 1.685 6.132 14DOPC OS7 761 0.511 1.755 6.145 14DOPCP8 762 0.628 1.683 6.064 14DOPC OM9 763 0.640 1.548 6.123 14DOPC OM10 764 0.747 1.771 6.072 14DOPC OS11 765 0.576 1.681 5.913 14DOPC C12 766 0.591 1.806 5.845 14DOPC C13 767 0.470 1.901 5.846 14DOPC OS14 768 0.364 1.830 5.782 14DOPC C15 769 0.247 1.869 5.833 14DOPC O16 770 0.238 1.946 5.927 14DOPC C17 771 0.123 1.815 5.762 14DOPC C18 772 -0.004 1.897 5.786 14DOPC C19 773 -0.138 1.837 5.744 14DOPC C20 774 -0.147 1.817 5.593 14DOPC C21 775 -0.196 1.678 5.552 14DOPC C22 776 -0.181 1.637 5.406 14DOPC C23 777 -0.252 1.722 5.301 14DOPC C24 778 -0.241 1.664 5.163 14DOPC C25 779 -0.267 1.738 5.054 14DOPC C26 780 -0.312 1.881 5.044 14DOPC C27 781 -0.368 1.918 4.907 14DOPC C28 782 -0.266 1.941 4.795 14DOPC C29 783 -0.324 2.015 4.674 14DOPC C30 784 -0.377 1.920 4.567 14DOPC C31 785 -0.377 1.984 4.428 14DOPC C32 786 -0.439 1.894 4.321 14DOPC C33 787 -0.358 1.890 4.191 14DOPC C34 788 0.490 2.037 5.777 14DOPC OS35 789 0.541 2.029 5.644 14DOPC C36 790 0.591 2.142 5.593 14DOPC O37 791 0.595 2.252 5.646 14DOPC C38 792 0.674 2.092 5.476 14DOPC C39 793 0.818 2.145 5.475 14DOPC C40 794 0.906 2.056 5.387 14DOPC C41 795 1.042 2.123 5.364 14DOPC C42 796 1.160 2.029 5.339 14DOPC C43 797
Re: [gmx-users] Re: Charmm 36 forcefield with verlet cut-off scheme
Note that the group scheme does not reproduce the (AFAIK unpublished) CHARMM switching scheme, either. Mark On Fri, Sep 20, 2013 at 4:26 AM, Justin Lemkul jalem...@vt.edu wrote: On 9/19/13 9:55 PM, akk5r wrote: Thanks Justin. I was told that the vdwtype = switch was an essential component of running Charmm36. Is that not the case? It is, but I suppose one can achieve a similar effect with the Verlet scheme. You can certainly use the traditional CHARMM settings if you use the group scheme, instead. The vdw-modifier setting should give you a comparable result, but I have never tried it myself. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] modify nsteps in an existing tpr file
Indeed - your question was fair, and no undue criticism pertained! :-) If you are trying to reproduce something, you must expect .tpr differences between 4.0.x and 4.6.y. I illustrated the change that has taken place in how VDW parameters are used internally in 4.6, and how that is distinct from the (presumably) unchanged description of those parameters. How and where to document this kind of thing so that people who need it can find it and those who don't need it don't drown in paper is an impossible problem! Cheers, Mark On Wed, Sep 18, 2013 at 8:34 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: It is only a simple question, not a criticism of any kind. I'm sure there may be perfect reasons to choose one implementation over another. To someone who is not familiar with the history of gmx development, it is something to be aware of. That's all. On Wed, Sep 18, 2013 at 4:56 PM, Mark Abraham mark.j.abra...@gmail.comwrote: Implementation and description of a model physics are two different things. You could compute KE of a particle with 0.5 * m * v^2, but if the mass is used nowhere else, why wouldn't you pre-multiply the mass by 0.5? Mark On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: hmm, does that mean the gmx force field file format or specifications are not backward compatible? On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham mark.j.abra...@gmail.com wrote: There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: That -om mechanism has been broken for about a decade
Re: [gmx-users] Error while simulating Protein in SDS/Water
Look at the numbers, count the number of atoms you expect in each moleculetype, and work out what the mismatch is. Mark On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl knnar...@sssihl.edu.in wrote: Dear GMX users, I am trying to simulate a protein in SDS/Water box. 1. No problems with pdb2gmx - .gro file and .top files were generated. /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/ selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 2. Created a Cubic box using editconf /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/ 3. Then solvated the system using genbox genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o protein_solv.gro -p topol.top 4. After this step I looked at the topol.top file and I found that it was not fully updated and so I manually updated by adding no. of SDS molecules under [ molecules ] section at the very end. Also I added #include sds.itp whereever it was required. In fact I followed the discussion between Justin, Mark and Anna Marabotti at the following link: http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html and did everything that was suggested. 5. When I use grompp after the step 4 grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr This is where I am getting a Fatal Error saying that the number of Co-ordinates in protein_solv.gro do not match with the number of co-ordinates in topol.top. Could you please help regarding this... Please give me your valuable suggestions. With Thanks and Best Regards Naresh -- View this message in context: http://gromacs.5086.x6.nabble.com/Error-while-simulating-Protein-in-SDS-Water-tp5011282.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] modify nsteps in an existing tpr file
That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm new to Gromacs. So apologies if this question is too simple. I downloaded top/tpr files from the supplementary material of a published paper. The nsteps set in the tpr file is 100ns. I wish to do a small test run. Is there any way I can modify that? I've tried to create a mdp file that best matches the parameters found through gmxdump, but it gives me a lot of LINCS error. I can upload the mdp file and gmxdump file if you are kind to help. Thanks in advance. Best regards, -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Guanglei Cui -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] BGQ compilation with verlet kernels: #include file kernel_impl.h not found.
Thanks for the follow up. The take-home lesson is that building for BlueGene/Q is unlike building for the usual homogenous x86 cluster. You still need an MPI and non-MPI build, but the latter should be targeted at the front end (Linux on PowerPC, usually), unless/until GROMACS tools acquire MPI functionality useful on a BlueGene/Q scale. Mark On Wed, Sep 18, 2013 at 2:07 AM, Christopher Neale chris.ne...@mail.utoronto.ca wrote: Indeed, it works just fine when I compile with mpi. I never thought to check that. My usual procedure is to compile the whole package without mpi and then to compile mdrun with mpi. Thanks for the help Mark. Here is the compilation script that worked for me. module purge module load vacpp/12.1 xlf/14.1 mpich2/xl module load cmake/2.8.8 module load fftw/3.3.2 export FFTW_LOCATION=/scinet/bgq/Libraries/fftw-3.3.2 cmake ../source/ \ -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C \ -DCMAKE_PREFIX_PATH=$FFTW_LOCATION \ -DCMAKE_INSTALL_PREFIX=$(pwd) \ -DGMX_X11=OFF \ -DGMX_MPI=ON \ -DGMX_PREFER_STATIC_LIBS=ON make -j 16 make install -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] modify nsteps in an existing tpr file
There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.comwrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. Is it possible to dump the parameters in the tpr file to a mdp file? On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham mark.j.abra...@gmail.com wrote: mdrun -nsteps in 4.6 overrides the number of steps in the .tpr Mark On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Dear GMX users, I'm new to Gromacs. So apologies if this question is too simple. I downloaded top/tpr files from the supplementary material of a published paper. The nsteps set in the tpr file is 100ns. I wish
Re: [gmx-users] modify nsteps in an existing tpr file
Implementation and description of a model physics are two different things. You could compute KE of a particle with 0.5 * m * v^2, but if the mass is used nowhere else, why wouldn't you pre-multiply the mass by 0.5? Mark On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: hmm, does that mean the gmx force field file format or specifications are not backward compatible? On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham mark.j.abra...@gmail.comwrote: There are technical differences between versions about how the VDW parameters are computed. You should not expect .tpr equivalence between minor version changes such as 4.0 and 4.6. You need to compile a 4.0.x grompp to see if your setup is equivalent, but having done so you should be able to use the same inputs to 4.6 grompp and get a correct simulation with 4.6 mdrun. Mark On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: Thanks. gmxcheck is quite helpful. Here is part of the output. It turns out the difference is mainly in the force field parameters, which indicates the top file provided may not be the one used to produce the tpr file. Perhaps it is best to contact the authors, unless the difference is due to certain changes between gmx 4.0.x and gmx 4.6.3. inputrec-nsteps (5000 - 5000) inputrec-nstcalclr (5 - 0) inputrec-nstdhdl (1 - 50) inputrec-fepvals-init_fep_state ( 0.0e+00 - -1.0e+00) inputrec-fepvals-lambda_neighbors[1] (0 - 1) inputrec-fepvals-sc_power (0 - 1) inputrec-dihre_fc (1.00e+03 - 0.00e+00) inputrec-grpopts.ngtc (4 - 1) inputrec-grpopts.ngener (4 - 1) inputrec-grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) idef-iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[96]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 idef-iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 idef-iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 idef-iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 idef-iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 idef-iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 idef-iparam[174]1: c6= 3.8381e-03, c12= 2.83264171e-06 idef-iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 idef-iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 idef-iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 idef-iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 idef-iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 idef-iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 idef-iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 idef-iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 idef-iparam[180]2: c6= 2.05496373e-24, c12= 0.e+00 idef-iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 idef-iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 idef-iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 ... On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham mark.j.abra...@gmail.com wrote: That -om mechanism has been broken for about a decade, unfortunately. You will need to include the file, or post a link a file, not attach it, if you want users of this list to see it. gmxcheck to compare your new and old .tpr files is useful to see what you might need in the new .mdp file to reproduce the first one. Note that grompp -c yourold.tpr is the best way to get the same starting coordinates. Mark On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui amber.mail.arch...@gmail.com wrote: gmxdump -om writes out a mdp file based on the tpr, but that is not read by grompp. I tried to change or comment out mdp options that are not recognized by grompp. It is attached here. The simulation soon crashes with LINCS errors after 25 steps, while the original tpr runs properly. I'm not sure what's missing here. On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham mark.j.abra...@gmail.com wrote: No. Theoretically useful, but not implemented. Mark On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui amber.mail.arch...@gmail.com
Re: [gmx-users] How to restart the crashed run
http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests the 3.x-era restart strategy when checkpoint files are unavailable. But if you simply have no output files, then you have no ability to restart. Mark On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi my friends please help me i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near the end of the simulation How to restart the crashed run? in the gromacs.org following comment has been proposed mdrun -s topol.tpr -cpi state.cpt but i don't have state.cpt in my folder. I need urgent help Thank you very much -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Difficulties with MPI in gromacs 4.6.3
On Tue, Sep 17, 2013 at 2:04 AM, Kate Stafford kastaff...@gmail.com wrote: Hi all, I'm trying to install and test gromacs 4.6.3 on our new cluster, and am having difficulty with MPI. Gromacs has been compiled against openMPI 1.6.5. The symptom is, running a very simple MPI process for any of the DHFR test systems: orterun -np 2 mdrun_mpi -s topol.tpr produces this openMPI warning: -- An MPI process has executed an operation involving a call to the fork() system call to create a child process. Open MPI is currently operating in a condition that could result in memory corruption or other system errors; your MPI job may hang, crash, or produce silent data corruption. The use of fork() (or system() or other calls that create child processes) is strongly discouraged. The process that invoked fork was: Local host: hb0c1n1.hpc (PID 58374) MPI_COMM_WORLD rank: 1 If you are *absolutely sure* that your application will successfully and correctly survive a call to fork(), you may disable this warning by setting the mpi_warn_on_fork MCA parameter to 0. -- Hmm. That warning is a known issue in some cases: http://www.open-mpi.org/faq/?category=openfabrics#ofa-fork but should not be an issue for the above mdrun command, since it should call none of popen/fork/system. You might like to try some of the diagnostics on that page. ...which is immediately followed by program termination by the cluster queue due to exceeding the allotted memory for the job. This behavior persists no matter how much memory I use, up to 16GB per thread, which is surely excessive for any of the DHFR benchmarks. Turning the warning off, of course, simply suppresses the output, but doesn't affect the memory usage. I can think of no reason for or past experience of this behaviour. Is it possible for you to run mdrun_mpi in a debugger and get a call stack trace to help us diagnose? The openMPI install works fine with other MPI-enabled programs, including gromacs 4.5.5, so the problem is specific to 4.6.3. The thread-MPI version of 4.6.3 is also fine. OK, thanks, good diagnosis. Some low-level stuff did get refactored after 4.6.1. I don't think that will be the issue here, but you could see if it produces the same symptoms / magically works. The 4.6.3 MPI executable was compiled with: cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/nfs/apps/cuda/5.5.22 -DGMX_MPI=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON But the presence of the GPU or static libs related flags seems not to affect the behavior. The gcc version (4.4 or 4.8) doesn't matter either. Any insight as to what I'm doing wrong here? So far I'd say the problem is not of your making :-( Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Standard errors
Standard error and standard deviation measure different things. Please consult a general work on reporting scientific results. Mark On Mon, Sep 16, 2013 at 7:40 AM, afsaneh maleki maleki.afsa...@gmail.com wrote: Dear all I would like to calculate the standard deviation (as the error bar) for dV/dlanda.xvg file. I used g_analyze command as the following: g_analyze -ffree_bi_0.9.xvg -av average_0.9 I got: set average *standard deviation* *std. dev. / sqrt(n-1)*… SS16.053822e+01 3.062230e+01 1.936724e-02… Is the amount of in third (standard deviation) or fourth column (std. dev. / sqrt(n-1) ) better than to use as the standard errors? I want to draw dG/d lambda via lambda and show error bar for free energy. Thanks in advance Afsaneh -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Re: Seeking solution for the error Atom OXT in residue TRP 323 was not found in rtp entry TRP with 24 atoms while sorting atoms.
Please answer all of Justin's questions. What is in the PDB file - what should the C terminus be! Mark On Tue, Sep 17, 2013 at 2:27 AM, Santhosh Kumar Nagarajan santhoshraja...@gmail.com wrote: I have tried it Tsjerk.. But the same error is shown again.. - Santhosh Kumar Nagarajan MTech Bioinformatics SRM University Chennai India -- View this message in context: http://gromacs.5086.x6.nabble.com/Seeking-solution-for-the-error-Atom-OXT-in-residue-TRP-323-was-not-found-in-rtp-entry-TRP-with-24-at-tp5011015p5011224.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to restart the crashed run
Hi, Please keep discussion on the mailing list. If you have a .cpt file that is not called state.cpt, then you must have asked for the checkpoint file to be named md.cpt in your original mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the default filename (and mostly there is no reason to change that). Simply use md.cpt, now that you have it :-) Mark On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: I have md.cpt but I don't have restart my run What is the purpose of the state.cpt file? thank you so much From: Mark Abraham mark.j.abra...@gmail.com To: Mahboobeh Eslami mahboobeh.esl...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, September 17, 2013 9:36 AM Subject: Re: [gmx-users] How to restart the crashed run http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests the 3.x-era restart strategy when checkpoint files are unavailable. But if you simply have no output files, then you have no ability to restart. Mark On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi my friends please help me i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near the end of the simulation How to restart the crashed run? in the gromacs.org following comment has been proposed mdrun -s topol.tpr -cpi state.cpt but i don't have state.cpt in my folder. I need urgent help Thank you very much -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] How to restart the crashed run
You named them last time you ran mdrun, either explicitly or with -deffnm. Do the same. Mark On Tue, Sep 17, 2013 at 3:19 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: when i use following omment for restart mdrun -s md.tpr -cpi md.cpt i get following error Output file appending has been requested, but some output files listed in the checkpoint file md.cpt are not present or are named differently by the current program: output files present: md.log output files not present or named differently: md.trr md.edr but i have md.trr and md.edr in my folder. thank you so much - Forwarded Message - From: Mark Abraham mark.j.abra...@gmail.com To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, September 17, 2013 11:22 AM Subject: Re: [gmx-users] How to restart the crashed run Hi, Please keep discussion on the mailing list. If you have a .cpt file that is not called state.cpt, then you must have asked for the checkpoint file to be named md.cpt in your original mdrun command (e.g. with mdrun -cpo md). state.cpt is simply the default filename (and mostly there is no reason to change that). Simply use md.cpt, now that you have it :-) Mark On Tue, Sep 17, 2013 at 2:49 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: I have md.cpt but I don't have restart my run What is the purpose of the state.cpt file? thank you so much From: Mark Abraham mark.j.abra...@gmail.com To: Mahboobeh Eslami mahboobeh.esl...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Sent: Tuesday, September 17, 2013 9:36 AM Subject: Re: [gmx-users] How to restart the crashed run http://www.gromacs.org/Documentation/How-tos/Doing_Restarts suggests the 3.x-era restart strategy when checkpoint files are unavailable. But if you simply have no output files, then you have no ability to restart. Mark On Tue, Sep 17, 2013 at 1:59 AM, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi my friends please help me i did 20 ns simulation by gromacs 4.5.5 but the power was shut down near the end of the simulation How to restart the crashed run? in the gromacs.org following comment has been proposed mdrun -s topol.tpr -cpi state.cpt but i don't have state.cpt in my folder. I need urgent help Thank you very much -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
