Re: [gmx-users] Question about make_ndx and g_angle
Dear Changwoon, why are you using ./make_ndx instead of make_ndx? Did you try to use the command without ./? Regards El jue, 07-11-2013 a las 14:12 -0800, Chang Woon Jang escribió: Dear Users, I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try the following command, there is an error message. ./make.ndx -f data.pdb ./make_ndx: error while loading shared libraries: libcudart.so.4:cannot open shared object file: No such file or directory Do I need cuda library in order to use make_ndx and g_angle ? Thanks. Best regards, Changwoon Jang -- 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] after using ACPYPE , GROMACS OPLS itp file generated an atom type like opls_x with mass 0.000
Hi, this feature is really really experimental and should indeed be avoided. If opls you want, then give a try with http://www.aribeiro.net.br/mktop/ Alan On 8 November 2013 04:42, aditya sarma adityasrm...@gmail.com wrote: Hi, i was trying to generate topology for p-phenylene vinylene polymer for OPLS forcefield using acpype . The itp file i got has the atomtype opls_x with mass 0.00. Is there any way to rectify this? After reading through how acpype works i found out this was one of the possible errors but there was no solution to it. This is a part of the itp file generated: [ atoms ] ; nr type resi res atom cgnr charge mass ; qtot bond_type 1 opls_145 1 LIG C1-0.117500 12.01100 ; qtot -0.118 CA 2 opls_145 1 LIGC12-0.055800 12.01100 ; qtot -0.173 CA 3 opls_145 1 LIGC23-0.117500 12.01100 ; qtot -0.291 CA 4 opls_145 1 LIGC34-0.131000 12.01100 ; qtot -0.422 CA 5 opls_145 1 LIGC45-0.125000 12.01100 ; qtot -0.547 CA 6 opls_145 1 LIGC56-0.131000 12.01100 ; qtot -0.678 CA 7 opls_x 1 LIGC67-0.099200 0.0 ; qtot -0.777 x 8 opls_x 1 LIGC78-0.105200 0.0 ; qtot -0.882 x 9 opls_145 1 LIGC89-0.048800 12.01100 ; qtot -0.931 CA 10 opls_145 1 LIGC9 10-0.119500 12.01100 ; qtot -1.051 CA 11 opls_145 1 LIG C10 11-0.118500 12.01100 ; qtot -1.169 CA 12 opls_145 1 LIG C11 12-0.051800 12.01100 ; qtot -1.221 CA 13 opls_145 1 LIG C12 13-0.118500 12.01100 ; qtot -1.339 CA 14 opls_145 1 LIG C13 14-0.119500 12.01100 ; qtot -1.459 CA 15 opls_x 1 LIG C14 15-0.101200 0.0 ; qtot -1.560 x 16 opls_x 1 LIG C15 16-0.103200 0.0 ; qtot -1.663 x 17 opls_145 1 LIG C16 17-0.049800 12.01100 ; qtot -1.713 CA 18 opls_145 1 LIG C17 18-0.119500 12.01100 ; qtot -1.833 CA 19 opls_145 1 LIG C18 19-0.119000 12.01100 ; qtot -1.952 CA 20 opls_145 1 LIG C19 20-0.050800 12.01100 ; qtot -2.002 CA 21 opls_145 1 LIG C20 21-0.119000 12.01100 ; qtot -2.121 CA 22 opls_145 1 LIG C21 22-0.119500 12.01100 ; qtot -2.241 CA 23 opls_x 1 LIG C22 23-0.102200 0.0 ; qtot -2.343 x 24 opls_x 1 LIG C23 24-0.102200 0.0 ; qtot -2.445 x 25 opls_145 1 LIG C24 25-0.050800 12.01100 ; qtot -2.496 CA 26 opls_145 1 LIG C25 26-0.119000 12.01100 ; qtot -2.615 CA 27 opls_145 1 LIG C26 27-0.119000 12.01100 ; qtot -2.734 CA 28 opls_145 1 LIG C27 28-0.050800 12.01100 ; qtot -2.785 CA 29 opls_145 1 LIG C28 29-0.119000 12.01100 ; qtot -2.904 CA 30 opls_145 1 LIG C29 30-0.119000 12.01100 ; qtot -3.023 CA 31 opls_x 1 LIG C30 31-0.102200 0.0 ; qtot -3.125 x 32 opls_x 1 LIG C31 32-0.102200 0.0 ; qtot -3.227 x 33 opls_145 1 LIG C32 33-0.050800 12.01100 ; qtot -3.278 CA 34 opls_145 1 LIG C33 34-0.119000 12.01100 ; qtot -3.397 CA 35 opls_145 1 LIG C34 35-0.119000 12.01100 ; qtot -3.516 CA 36 opls_145 1 LIG C35 36-0.050800 12.01100 ; qtot -3.567 CA 37 opls_145 1 LIG C36 37-0.119000 12.01100 ; qtot -3.686 CA 38 opls_145 1 LIG C37 38-0.119000 12.01100 ; qtot -3.805 CA 39 opls_x 1 LIG C38 39-0.102200 0.0 ; qtot -3.907 x 40 opls_x 1 LIG C39 40-0.102200 0.0 ; qtot -4.009 x 41 opls_145 1 LIG C40 41-0.050800 12.01100 ; qtot -4.060 CA 42 opls_145 1 LIG C41 42-0.119000 12.01100 ; qtot -4.179 CA 43 opls_145 1 LIG C42 43-0.119500 12.01100 ; qtot -4.299 CA 44 opls_145 1 LIG C43 44-0.049800 12.01100 ; qtot -4.348 CA 45 opls_145 1 LIG C44 45-0.119500 12.01100 ; qtot -4.468 CA 46 opls_145 1 LIG C45 46-0.119000 12.01100 ; qtot -4.587 CA 47 opls_x 1 LIG C46 47-0.103200 0.0 ; qtot -4.690 x 48 opls_x 1 LIG C47 48-0.101200 0.0 ; qtot -4.791 x -- 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
Re: [gmx-users] TFE-water simulation
Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -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 -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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] TFE-water simulation
Hello again, That depends on the peptide. There is no general answer. I am starting with a linear conformations, but that's because I'm working with intrinsically disordered proteins. That's as far as I can go regarding telling you about what I'm doing. I'm not at liberty to discuss these things, it's not public yet, sorry. Best regards, João On Fri, Nov 8, 2013 at 11:32 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Should I start with helical peptides and see if it maintains the helicity or I can start with random coil? Do random coil peptides take long simulation time to form helical peptides? any help on this will be appreciated. On Tue, Nov 5, 2013 at 12:25 AM, Archana Sonawani-Jagtap ask.arch...@gmail.com wrote: Thanks Joao Henriques for helping me with the steps. On Nov 4, 2013 3:18 PM, João Henriques joao.henriques.32...@gmail.com wrote: Hello Archana, I'm also toying with a TFE-water system, therefore I am also a newbie. This is what I am doing, I hope it helps: 1) Since I'm using G54A7 I created a TFE.itp using GROMOS parameters (I don't use PRODGR, see why in DOI: 10.1021/ci100335w). 2) Do the math and check how many molecules of TFE you're going to need for a given v/v TFE-water ratio and a given simulation box volume. 3) Build box with the correct size. 4) Randomly insert correct number of TFE molecules. 5) Solvate. 6) Insert protein. Hopefully, the amount of TFE and water molecules that will be deleted in inserting the protein in the final step will be proportional, given that the TFE molecules are well distributed. I've tried many different ways of doing this and it's always impossible to maintain a perfect TFE-water ratio, no matter the order and manner of insertion of each system component. I've also never been able to insert the correct number of waters after the TFE. My calculations predict a higher number, but the solvation algorithm can't find enough space for them. In sum, either you place each molecule by hand and you spend a life time building the system, or you just make a few compromises and deal with it. I ended up going with the former as I have a limited amount of time on my hands and I am aware of the approximations I am doing. Best regards, João Henriques PhD student Division of Theoretical Chemistry Lund University Lund, Sweden joao.henriq...@teokem.lu.se http://www.teokem.lu.se/~joaoh/ On Thu, Oct 24, 2013 at 7:15 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/24/13 1:13 PM, Archana Sonawani-Jagtap wrote: Dear Justin, I have not constructed the system but I have downloaded it from ATB website. To maintain the number of TFE and water molecules(1:1 v/v) in the system (I don't want to add extra water molecules) I tried many options in genbox but still it adds 678 water molecules. Can you provide me some hint? Not without seeing your actual command(s). Is their need to remove periodicity of this pre-equilibrated system as in case of lipids? No idea. Are the molecules broken in the initial configuration? -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 -- Archana Sonawani-Jagtap Senior Research Fellow, Biomedical Informatics Centre, NIRRH (ICMR), Parel Mumbai, India. 9960791339 -- 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
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
Re: [gmx-users] Problem compiling Gromacs 4.6.3 with CUDA
Ok, you convinced me. I'll really give it a try. I'm following this throw the suposition that openMP implementation on intel compilers is not as good as GNU compilers. I already tested intel openMP in our cluster, and it just sucked in comparison to the pure MPI compilation. Let's hope I can make it work together with the IMPI. I don't want to install openmpi as just a user also (did it a long time ago as root, not in limited space). Thanks again! On Fri, Nov 8, 2013 at 9:21 AM, Mark Abraham mark.j.abra...@gmail.comwrote: On Fri, Nov 8, 2013 at 12:02 AM, Jones de Andrade johanne...@gmail.com wrote: 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
[gmx-users] Reg error in Compilation Of Gromacs 4.6.2
Dear Justin Thank you for your Previous reply, I am trying to Install gromacs 4.6.2 in a cluster having centos OS with teh Following Command I got following error cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON CMake Warning at CMakeLists.txt:785 (message): No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance). CMake Warning at CMakeLists.txt:802 (message): No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance). CMake Error at CMakeLists.txt:872 (gmx_test_avx_gcc_maskload_bug): GMX_TEST_AVX_GCC_MASKLOAD_BUG Macro invoked with incorrect arguments for macro named: GMX_TEST_AVX_GCC_MASKLOAD_BUG -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring incomplete, errors occurred! The Aforesaid Error Indicates What is the Lack ? I Think I need Latest Compiler (Please Indicate Version) is it Correct Not? How to solve the problem What are Prerequestite i need ? Already Gromacs 4.5.5 has been installed sucessfully Thanks in Advance -- 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
On Fri, Nov 8, 2013 at 7:18 PM, Mark Abraham mark.j.abra...@gmail.comwrote: 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
Re: [gmx-users] Re: CHARMM .mdp settings for GPU
On 11/7/13 11:32 PM, Rajat Desikan wrote: Dear All, The setting that I mentioned above are from Klauda et al., for a POPE membrane system. They can be found in charmm_npt.mdp in lipidbook (link below) http://lipidbook.bioch.ox.ac.uk/package/show/id/48.html Is there any reason not to use their .mdp parameters for a membrane-protein system? Justin's recommendation is highly valued since I am using his forcefield. Justin, your comments please Careful now, it's not my forcefield. I derived only a very small part of it :) To summarize: Klauda et al., suggest rlist = 1.0 rlistlong= 1.4 rvdw_switch = 0.8 vdwtype= Switch coulombtype = pme DispCorr= EnerPres ;only usefull with reaction-field and pme or pppm rcoulomb = 1.0 rcoulomb_switch= 0.0 rvdw = 1.2 Justin's recommendation (per mail above) vdwtype = switch rlist = 1.2 rlistlong = 1.4 rvdw = 1.2 rvdw-switch = 1.0 rcoulomb = 1.2 The differences between these two sets of run parameters are very small, dealing mostly with Coulomb and neighbor searching cutoffs. I would suspect that any difference between simulations run with these two settings would be similarly small or nonexistent, given that rcoulomb is a bit flexible when using PME. The value of rlist is rarely mentioned in papers, so it is good that the authors have provided the actual input file. Previous interpretation of CHARMM usage generally advised setting rcoulomb = 1.2 to remain consistent with the original switching/shifting functions. That setting becomes a bit less stringent when using PME. -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
Re: [gmx-users] Reg error in Compilation Of Gromacs 4.6.2
On 11/8/13 7:44 AM, vidhya sankar wrote: Dear Justin Thank you for your Previous reply, I am trying to Install gromacs 4.6.2 in a cluster having centos OS with teh Following Command I got following error cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_DOUBLE=ON CMake Warning at CMakeLists.txt:785 (message): No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance). CMake Warning at CMakeLists.txt:802 (message): No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance). CMake Error at CMakeLists.txt:872 (gmx_test_avx_gcc_maskload_bug): GMX_TEST_AVX_GCC_MASKLOAD_BUG Macro invoked with incorrect arguments for macro named: GMX_TEST_AVX_GCC_MASKLOAD_BUG -- The GROMACS-managed build of FFTW 3 will configure with the following optimizations: --enable-sse2 -- Configuring incomplete, errors occurred! The Aforesaid Error Indicates What is the Lack ? I Think I need Latest Compiler (Please Indicate Version) is it Correct Not? How to solve the problem What are Prerequestite i need ? You haven't said what compiler you're using, but suffice it to say based on the above messages, it's too old to make use of the best optimizations. Either upgrade the compiler or accept SSE4.1 optimization instead of AVX. -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
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
[gmx-users] Looking for advice on Monte Carlo simulations, please
Hi, I have been using Gromacs for my MD liquid simulations for about 2 years now, and, of course, it has been working great! Now, in the current part of my project, I am looking at liquid structure, not dynamics. Of course, one can analyze liquid structure by simply analyzing an MD trajectory. I have run into some difficulties with sampling, however. I could try some special sampling techniques (umbrella sampling, replica exchange, etc.), but another thing that has been suggested to me is to try Monte Carlo simulations. Monte Carlo simulations, of course, do not model dynamics, but since I'm only interested in structure at this point, Monte Carlo might be a faster, less computationally expensive way to do sampling of possible liquid structures/configurations. It looks like, according to the Gromacs website, that a Monte Carlo integrator is in the process of being implemented in Gromacs (maybe for version 5.0 or so?). If that is possible and will be funded, that would be great, because I would just like to use my same force field, same parameters as I have for my MD simulations--but just now I want to use Monte Carlo to quickly generate (low-energy/high-probability) configurations. But, until Monte Carlo is implemented in Gromacs, do you have any suggestions of another package that I can use to do MC on my system? Perhaps there is some MC package out there that is somewhat similar to Gromacs, such that maybe I could write scripts to translate my system topology from Gromacs to the MC package? Do you have any experience or advice on Monte Carlo simulations? By the way, I hesitate to even ask questions like when is this or that feature going to be implemented in Gromacs?, because I know that the development of Gromacs is a huge project and that many people are spending lots of time and resources to continually add features! I am not yet very fluent in C/C++ and am not much of a programmer. I am more of a chemist/simulator. So I just want to thank you all for all your work on making Gromacs what it is! Thanks! Andrew DeYoung Carnegie Mellon University -- 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] Looking for advice on Monte Carlo simulations, please
The only open source Monte Carlo package I have every used or now of is MCCS Towhee: http://towhee.sourceforge.net/ Andrew On 11/08/2013 11:23 AM, Andrew DeYoung wrote: Hi, I have been using Gromacs for my MD liquid simulations for about 2 years now, and, of course, it has been working great! Now, in the current part of my project, I am looking at liquid structure, not dynamics. Of course, one can analyze liquid structure by simply analyzing an MD trajectory. I have run into some difficulties with sampling, however. I could try some special sampling techniques (umbrella sampling, replica exchange, etc.), but another thing that has been suggested to me is to try Monte Carlo simulations. Monte Carlo simulations, of course, do not model dynamics, but since I'm only interested in structure at this point, Monte Carlo might be a faster, less computationally expensive way to do sampling of possible liquid structures/configurations. It looks like, according to the Gromacs website, that a Monte Carlo integrator is in the process of being implemented in Gromacs (maybe for version 5.0 or so?). If that is possible and will be funded, that would be great, because I would just like to use my same force field, same parameters as I have for my MD simulations--but just now I want to use Monte Carlo to quickly generate (low-energy/high-probability) configurations. But, until Monte Carlo is implemented in Gromacs, do you have any suggestions of another package that I can use to do MC on my system? Perhaps there is some MC package out there that is somewhat similar to Gromacs, such that maybe I could write scripts to translate my system topology from Gromacs to the MC package? Do you have any experience or advice on Monte Carlo simulations? By the way, I hesitate to even ask questions like when is this or that feature going to be implemented in Gromacs?, because I know that the development of Gromacs is a huge project and that many people are spending lots of time and resources to continually add features! I am not yet very fluent in C/C++ and am not much of a programmer. I am more of a chemist/simulator. So I just want to thank you all for all your work on making Gromacs what it is! Thanks! Andrew DeYoung Carnegie Mellon University -- Andrew S. Paluch, PhD Department of Chemical, Paper, and Biomedical Engineering Miami University paluc...@miamioh.edu (513) 529-0784 -- 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] Question about make_ndx and g_angle
Dear Riccardo Concu, The reason is that I used the make_ndx file in the working directory. Now, I solved that problem with installing gromacs as following cmake .. -DGMX_BUILD_OWN_FFTW=Off Anyway, I appreciate your comment. Best regards, Changwoon Jang On Friday, November 8, 2013 3:31 AM, Riccardo Concu ric.co...@gmail.com wrote: Dear Changwoon, why are you using ./make_ndx instead of make_ndx? Did you try to use the command without ./? Regards El jue, 07-11-2013 a las 14:12 -0800, Chang Woon Jang escribió: Dear Users, I am using openSUSE 12.3 and try to use make_ndx and g_angle. When I try the following command, there is an error message. ./make.ndx -f data.pdb ./make_ndx: error while loading shared libraries: libcudart.so.4:cannot open shared object file: No such file or directory Do I need cuda library in order to use make_ndx and g_angle ? Thanks. Best regards, Changwoon Jang -- gmx-users mailing list gmx-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: free energy
Dear Kieu Thu Thanks for your comment about free energy. Unfortunately, I could not send a email to Paissoni Cristina in the Gromacs Forum. Could you give me email address of Paissoni Cristina? Finding a tool for calculation MM/PBSA with Gromacs is very vital for me. Best Regards Kiana -- View this message in context: http://gromacs.5086.x6.nabble.com/free-energy-tp5012246p5012363.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] Simulation box size, LIE and PME
Greetings The discussion list had helped me about understanding what to do when I want to calculate binding free energy using LIE after doing MD simulation using PME. Now I need your help about choosing the simulation box size for ligand and complex. I used -d 1.0 in editconf for the complex simulation and -d 1.6 for the ligand simulation. Are this values ok? Should I use a different value of -d for the ligand simulation? 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] Re: Ligand simulation for LIE with PME
Greetings again If I use a salt concentration for neutralizing the protein-ligand complex and run MD using PME, and the ligand is neutral, do I perform ligand MD simulation without adding any salt concentration? It could be relevant for LIE free energy calculation if I don't include salt in ligand (neutral) simulation, even when I simulate Protein-ligand system with salt? 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] Reaction field zero, ions, twin-range and LIE
Hello users For making a rerun of a MD simulation done with PME, but this time using Reaction field zero, do I eliminate the ions from the system, previously added to neutralize and ran with PME? What do you think about using a twin-range cut off instead of reaction field zero? I need to obtain precise Coul SR and Coul LR for LIE calculation. Thank you 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] Re: choosing force field
Sorry for the previous mistake. Instead of 53a7, the force field which I used was 53a6. On Fri, Nov 8, 2013 at 12:10 AM, Justin Lemkul [via GROMACS] ml-node+s5086n5012325...@n6.nabble.com wrote: On 11/7/13 12:14 PM, pratibha wrote: My protein contains metal ions which are parameterized only in gromos force field. Since I am a newbie to MD simulations, it would be difficult for me to parameterize those myself. Can you please guide me as per my previous mail which out of the two simulations should I consider more reliable-43a1 or 53a7? AFAIK, there is no such thing as 53A7, and your original message was full of similar typos, making it nearly impossible to figure out what you were actually doing. Can you indicate the actual force field(s) that you have been using in case someone has any ideas? The difference between 53A6 and 54A7 should be quite pronounced, in my experience, thus any guesses as to what 53A7 should be doing are not productive because I don't know what that is. -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 [hidden email] http://user/SendEmail.jtp?type=nodenode=5012325i=0 | (410) 706-7441 == -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=1 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 [hidden email]http://user/SendEmail.jtp?type=nodenode=5012325i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- If you reply to this email, your message will be added to the discussion below: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012325.html To unsubscribe from choosing force field, click herehttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_codenode=5012242code=a2Fwb29ycHJhdGliaGE3QGdtYWlsLmNvbXw1MDEyMjQyfC02NjkwNjY5MjU= . NAMLhttp://gromacs.5086.x6.nabble.com/template/NamlServlet.jtp?macro=macro_viewerid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml -- View this message in context: http://gromacs.5086.x6.nabble.com/choosing-force-field-tp5012242p5012370.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
