[gmx-users] how to calculate kinetic constant?

Hello: I've submit a simulation in gromacs, and I am just wondering how can we calculate kinetic constant for the ligand bound/ubound process? thanks a lot Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

[gmx-users] g_select problem

, is there anything wrong with my syntax? thank you very much. best Albert -- 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

Re: [gmx-users] g_select problem

which water molecules I would like to make. Do you have any idea how to do this correctly? thank you very much. best Albert -- 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

[gmx-users] identical results or exactly the same results?

Hello: I've got a md.tpr file generated by grompp, I am just wondering will the results be identical or would be exactly the same if I run it in different machine? thank you very much. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo

[gmx-users] is there any tool for flexibility?

' flexibility? thank you very much best Albert -- 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

Re: [gmx-users] is there any tool for flexibility?

On 09/01/2013 06:03 PM, Justin Lemkul wrote: Maybe g_msd or g_rmsf, but I don't think there's anything specifically designed to address water molecules, and the term flexibility can have far too many meanings ;) -Justin thanks a lot for kind messages. but there are a lot of water

Re: [gmx-users] problem of submitting job in HPC

/13 12:39 PM, Albert wrote: Hello: I am trying to use following command to run 4.6.3 in a HPC cluster: mpiexec -n 32 /opt/gromacs/4.6.3/bin/mdrun_mpi -dlb yes -v -s md.tpr -x md.xtc -o md.trr -g md.log -e md.edr md.info the 4.5.5 works fine in this machine with command

[gmx-users] efficiency in HPC

year for a job to be done while it only take 2 months in other machine. Does anybody have any idea where is the problem? thanks a lot Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

Re: [gmx-users] efficiency in HPC

On 08/29/2013 10:31 PM, Prentice Bisbal wrote: Albert, It looks like you are trying to compile for an IBM Power 7 system. What is the 'other machine' you are comparing it to, and did you use the same number of cores in each case? Prentice yes it is. here is the configurations: * 4 IBM

[gmx-users] work in 4.5.5 but failed in 4.6.1

--- Program grompp, VERSION 4.5.5 Source code file: grompp.c, line: 1584 Does anybody have any idea? thx Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] problem of submitting job in HPC

very much. best Albert -- 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

Re: [gmx-users] work in 4.5.5 but failed in 4.6.1

input .gro file. I don't understand, why this warning not appear in 4.6.3, but failed in 4.5.5 thank you very much Albert -- 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

Re: [gmx-users] work in 4.5.5 but failed in 4.6.1

the protein CA by genrest command, after that I delete the atoms which I don't want to restrain from output restrain.itp. Probably that's the problem? Maybe I should set the unwanted restrain atoms into 0 force constant instead of delete them from restrain.itp file? thx a lot Albert -- gmx

Re: [gmx-users] work in 4.5.5 but failed in 4.6.1

), it's possible that there's some weird hidden character that is causing the error. -Justin IC. the problem solved when I run command dos2unix. thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

[gmx-users] g_select problem

the command run without errors, but I noticed that the number of water molecules in the output file are all 0. When I visualize each frame, I observe a lot of water molecules within the defined region. Does anybody have any idea what's the problem? thx Albert -- gmx-users mailing listgmx-users

Re: [gmx-users] g_select problem

Hello Mark: thanks for kind advices. I checked my residues number carefully, and I didn't find anything wrong. However, I am not sure whether the syntax of my selection.dat is all right or not, since the documentation for this option is not well clarified. thank you very much Albert

Re: [gmx-users] g_select problem

but actually the water name in my system IS T3P and the atom name in the water model is O. I've double checked for this. thx Albert On 08/21/2013 04:59 PM, Teemu Murtola wrote: If that is really your selection, you are trying to select atoms that have both name T3P and O, which is clearly

Re: [gmx-users] g_select problem

and it works very well now. thanks all you guys. best Albert -- 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

[gmx-users] itp problem

#include helix.itp #endif when I run grompp, it claimed following warnings: WARNING 1 [file helix.itp, line 1]: Too few parameters on line (source file /home/albert/install/source/gromacs-4.6.3/src/kernel/toppush.c, line 1756) here is my helix.itp: ; position restraints for System

[gmx-users] GPU metadynamics

for this run: #0 I am just wondering how can we use multiple GPU for such kind of jobs? THX Albert -- 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

Re: [gmx-users] GPU metadynamics

On 08/15/2013 11:21 AM, Jacopo Sgrignani wrote: Dear Albert to run parallel jobs on multiple GPUs you should use something like this: mpirun -np (number of parallel sessions on CPU) mdrun_mpi .. -gpu_id so you will have 4 calculations for GPU. Jacopo thanks a lot

Re: [gmx-users] Re: Unkwown Keyword HILLS

On 08/14/2013 12:26 PM, Michael Shirts wrote: This is a plumed error, not a gromacs error. Gromacs never handles those keywords. Sent from my iPhone IC THX, it works now. I found some strange characters in the plumed.dat file. After delete them, it work now -- gmx-users mailing list

[gmx-users] how can we control output ?

0.08697 0.059861982 1.960 I am performing 200 ns MD simulations. The file probably will become too big I am just wondering how can we setup the frequency record for the HILL and COLVAR file? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org

[gmx-users] Unkwown Keyword HILLS

! PLUMED ERROR: Line 1 Unkwown Keyword HILLS ! ABORTING RUN --* thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] Re: Unkwown Keyword HILLS

Does anybody have any idea what's the problem? I use the tutorial example and I don't know why it doesn't work. THX On 08/13/2013 07:19 PM, Albert wrote: Dear: I am trying to run plumed with gromacs plugin. Here is my plumed.dat file which I defined two dihedral angels as cvs: *HILLS

Re: [gmx-users] Re: problem in g_membed

to see how many lipids did other people use. On 07/29/2013 10:31 AM, pavithrakb wrote: Thank you both of you (Justin and Albert) sir. Initially I was using dppc128 and now I changed to POPE 340 and still my protein (its a GPCR protein) protrude out of the membrane (the same region; two amino acids

[gmx-users] binding energy for membrane system

difficult thing is to evaluate the term from protein/lipids and protein/water part, since the system is heterogeneous instead of homogeneous. thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

Re: [gmx-users] How to calculate enthalpy

On 07/15/2013 10:20 AM, Dr. Vitaly Chaban wrote: Sure, you can. Dr. Vitaly V. Chaban I've got a question for it. Why the calculated entropy is negative? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at

[gmx-users] a question on energygrps

instead of running the simulation from beginning? I notice that there is a tool called g_lie can be used to evaluate protein/ligand binding, I am just wondering is there any paper on this tool? I don't find too much informations on gromacs manual. thank you very much Albert -- gmx-users

[gmx-users] cuda problem

set up for GMX_CUDA_STREAMSYNC? THX Albert -- 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

Re: [gmx-users] cuda problem

by the OpenMP library, disabling internal thread affinity best Albert -- 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

[gmx-users] why DGbind=0 ?

0 23000 0 24000 0 I am just wondering why the result is zero? thank you very much Albert -- 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

[gmx-users] why TIPS3P, why not TIP3P?

for their system. In this work, they performed 100+ us long time scaled MD simulation for a extremely large membrane protein. could anybody comment on this issue? THX a lot. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

Re: [gmx-users] why TIPS3P, why not TIP3P?

POPC+0.15M NaCl which is the most close system to physiology environment. Albert -- 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] Re: problem in g_membed

would be failed in the following step. You can visualize your system in VMD to double check. If it is not in the PBC BOX, you can use editconf -box to fix this issue. good luck. Albert On 07/08/2013 11:40 AM, Justin Lemkul wrote: On 7/7/13 10:52 PM, pavithrakb wrote: Dear Sir, Thanks so

Re: [gmx-users] 11-cis retinal topology problem

? thank you very much Albert -- 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

Re: [gmx-users] 11-cis retinal topology problem

--- I still don't know where is the problem. thank yo uvery much Albert -- 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

Re: [gmx-users] 11-cis retinal topology problem

); here is the angetypes section in the ffbonded.itp file which generated from the python scrips, to be honest I don't see anything bad thank you very much. Albert [ angletypes ] ; ijkfuncth0cthub0cub CT2CT2NCH15111.20669.440.00.0 HCR

Re: [gmx-users] 11-cis retinal topology problem

a fresh file, everything goes well now. best regards Albert -- 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

[gmx-users] 11-cis retinal topology problem

with messages: - Program grompp_mpi, VERSION 4.6.2 Source code file: /home/albert/Desktop/gromacs-4.6.2/src/kernel/topdirs.c, line: 106 Fatal error: Invalid angle type 0 For more information and tips for troubleshooting, please check the GROMACS website at http

Re: [gmx-users] 11-cis retinal topology problem

:9: error: expected ‘;’ before ‘}’ token make[2]: *** [src/kernel/CMakeFiles/gmxpreprocess.dir/topio.c.o] Error 1 make[2]: *** Waiting for unfinished jobs thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

Re: [gmx-users] 11-cis retinal topology problem

H16 Then I add this information into the aminoacide.rtp file. I don't know why it failed. It is expected to be treated as regular amino acid residue thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] GPU cannot be detected

Hello: I've installed Gromacs-4.6.2 in GPU cluster with following configurations: CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2-1.8-rhes6 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU

[gmx-users] charmm2gromacs-pvm.py error

= segments[1] IndexError: list index out of range although it generate a cgenff-2b7 folder, but all the files it generate are empty. thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] fftw compile error for 4.6.2

Hello: I am trying to compile Gromacs-4.6.2 for a GPU cluster with following command: CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2.amd/1.4 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU

Re: [gmx-users] fftw compile error for 4.6.2

/mvapich2.amd/1.4 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR=/export/cuda5.0 -DFFTWF_LIBRARY=/home/albert/install/fftw-3.3.3/lib/libfftw3f.so -DBUILD_SHARED_LIBS=OFF CMake Error: The following variables

Re: [gmx-users] fftw compile error for 4.6.2

I redirect the path into above path. best Albert -- 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

[gmx-users] another error compiling 4.6.2 in GPU cluster

Hello: I am using the following configuration to compile gromacs-4.6.2 in a GPU cluster: CC=icc FC=ifort F77=ifort CXX=icpc CMAKE_PREFIX_PATH=/export/intel/cmkl/include/fftw:/export/mpi/mvapich2-1.8-rhes6 cmake .. -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/albert/install/gromacs

Re: [gmx-users] fftw compile error for 4.6.2

advice is that you either use the code from git or wait for 4.6.3. Oh, my Lady GaGa... Do you have any idea when this new version would be released? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive

[gmx-users] a question concerning on entropy

. I am just wondering, is it possible to do this? thank you very much Albert -- 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] fftw compile error for 4.6.2

On 07/04/2013 07:59 PM, Mark Abraham wrote: I plan to release 4.6.3 tomorrow, once I've gotten some more urgent stuff off my plate:-). Mark thanks a lot for kind messages, Mark. It seems that Gromacs update more and more frequently Albert -- gmx-users mailing listgmx-users

[gmx-users] multiple chain restrain problem

command: genrestr -f gmx.pdb -p porsB it doesn't contains selection for chain thank you very much Albert -- 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

Re: [gmx-users] multiple chain restrain problem

advices. I solved this by extracting each chain into indivisual coordinate and make restrain based on them. best Albert -- 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

[gmx-users] problem with charmm2gromacs-pvm.py

-pvm.py, line 283, in module name = segments[1] IndexError: list index out of range thank you very much Albert -- 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

Re: [gmx-users] shall we use double precision?

. thank you very much Albert On 06/11/2013 08:55 AM, Mark Abraham wrote: Probably not. What does PLUMED documentation recommend? 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

[gmx-users] shall we use double precision?

Hello : I am going to use Gromacs with PLUMD plugin to perform Metadynamics. Since this methods involved in free energy calculations, I am just wondering is it necessary to introduce double precision Gromacs? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org

[gmx-users] why mass and charge is zero?

confused for this. Does anybody have any idea for it? thank you very much best Albert -- 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] why mass and charge is zero?

On 06/08/2013 06:56 PM, David van der Spoel wrote: the ones in the atoms section are the ones that are used UNLESS they are not given, in which case the defaults are used. IC. thank you very much. Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman

[gmx-users] GPU ECC question

options and the same version of intel compiler (2) why in machines both of physically installed two GTX590 cards, one of them was detected with 4 GPU while the other was claimed contains two GPU? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http

[gmx-users] GPU problem

submitted. Moreover, one of the job stopped after short of running, probably because of the CPU issue. I am just wondering, how can we distribute CPU when we run two GPU job in a single workstation? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] GPU problem

On 06/04/2013 11:22 AM, Chandan Choudhury wrote: Hi Albert, I think using -nt flag (-nt=16) with mdrun would solve your problem. Chandan thank you so much. it works well now. ALBERT -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users

[gmx-users] how to distribute CPU in GPU workstation?

you very much best Albert -- 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

Re: [gmx-users] GROMACS 4.6.2 released

it seems that Gromacs update quite frequently these days.. On 05/30/2013 05:42 PM, Mark Abraham wrote: Hi GROMACS users, GROMACS 4.6.2 is officially released. It contains numerous bug fixes, some simulation performance enhancements and some documentation updates. We encourage all users to

[gmx-users] g_select question

and there is only max. 12 water near 6A. However, I found that in almost all my trajectories, there are at least 16 water from the g_select output. I am just wondering, is there anything wrong of my defenition in selection.dat? thank you very much best Albert -- gmx-users mailing listgmx-users

[gmx-users] where can be obtain circled lipids bilayer?

Hello: I've got a question about where can be obtain circled lipids bilayer? like shown here: http://wwwuser.gwdg.de/~ggroenh/membed/vesicle.png thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

Re: [gmx-users] GPU job often stopped

the problem is still there... :-( On 04/29/2013 06:06 PM, Szilárd Páll wrote: On Mon, Apr 29, 2013 at 3:51 PM, Albertmailmd2...@gmail.com wrote: On 04/29/2013 03:47 PM, Szilárd Páll wrote: In that case, while it isn't very likely, the issue could be caused by some implementation

Re: [gmx-users] GPU job often stopped

in another GTX690 machine, it also goes well. I compiled Gromacs with the same options in that machine. thank you very much best Albert On 04/29/2013 01:19 PM, Szilárd Páll wrote: Have you tried running on CPUs only just to see if the issue persists? Unless the issue does not occur

Re: [gmx-users] GPU job often stopped

? best Albert -- 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

Re: [gmx-users] GPU job often stopped

On 04/29/2013 03:31 PM, Szilárd Páll wrote: The segv indicates that mdrun crashed and not that the machine was restarted. The GPU detection output (both on stderr and log) should show whether ECC is on (and so does the nvidia-smi tool). Cheers, -- Szilárd yes it was on: Reading file

Re: [gmx-users] GPU job often stopped

, were there any other processes using the GPU while mdrun was running? Cheers, -- Szilárd thanks for kind reply. There is no any other process when I am running Gromacs. do you mean I should set GMX_CUDA_STREAMSYNC in the job script like: export GMX_CUDA_STREAMSYNC=/opt/cuda-5.0 ? THX Albert

[gmx-users] can we use large timestep for membrane GPU simulation?

? What's more, Eric also shown the GLIC ion channel simulation with 150,000 atoms. E5-2690+GTX Titan can get up to 38ns/day. But he didn't talked about what's the timestep and cutoff. could anybody comment on this? thank you very much best Albert -- gmx-users mailing listgmx-users

[gmx-users] why files are so large?

it file size is negative? Moreover, my nstxout is very large, I don't know why the file is so big and no matter how did I change nstxout, nstvout, the files size doesn't change at all. it always claimed: This run will generate roughly 2791985478365075968 Mb of data thank you very much Albert

Re: [gmx-users] why files are so large?

. best Albert -- 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

[gmx-users] GPU job often stopped

). -- I can continue the jobs with mdrun option -append -cpi, but it still stopped from time to time. I am just wondering what's the problem? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please

[gmx-users] compile error

Dear: I've installed gromacs-4.6.1 in a GPU workstation with two GTX690. Here is my step: ./configure --prefix=/home/albert/install/openmpi-1.4.5 CC=icc CXX=icpc F77=ifort FC=ifort make make install cmake .. -DGMX_MPI=ON -DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DCUDA_TOOLKIT_ROOT_DIR

Re: [gmx-users] compile error

IC. it works very well now. thanks a lot Albert On 04/26/2013 08:01 PM, Szilárd Páll wrote: You got a warning at configure-time that the nvcc host compiler can't be set because the mpi compiler wrapper are used. Because of this, nvcc is using gcc to compile CPU code whick chokes on the icc

[gmx-users] GPU efficiency question

.: 3.0, ECC: no, stat: compatible why the -np 2 and -np 4 are the same efficiency? shouldn't it be faster for -np 4 ? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http

[gmx-users] _gpu_id failed

Hello: I am going to run gromacs with command: mpirun -np 4 mdrun_mpi -s em.tpr -c em.gro -v -g em.log -gpu_id #0, #2, #3, #4 but it failed with messages: Program mdrun_mpi, VERSION 4.6.1 Source code file: /home/albert/install/source/gromacs-4.6.1/src/gmxlib/statutil.c, line: 364 Fatal

Re: [gmx-users] GROMACS 4.6 with GPU acceleration (double

On 04/22/2013 08:40 AM, Mikhail Stukan wrote: Could you explain which hardware do you mean? As far as I know, K20X supports double precision, so I would assume that double precision GROMACS should be realizable on it. Really? But many people have discussed that the GPU version ONLY support

Re: [gmx-users] using CHARMM force field for organic molecule

On 04/22/2013 01:43 PM, Justin Lemkul wrote: There are several options, all external to Gromacs: https://www.paramchem.org/ http://www.swissparam.ch/ -Justin did paramchem support gromacs? As far as I know it only export in CHARMM format. Albert -- gmx-users mailing listgmx

Re: [gmx-users] how to direct log file correctly?

: mpirun -np 2 mdrun_mpi -v -s md.tpr -c md.gro -x md.xtc -g md.log md.info but it said: Invalid null command. thanks a lot Albert On 04/17/2013 05:33 PM, Justin Lemkul wrote: On 4/17/13 11:30 AM, Albert wrote: Hello: I found that each time I submit gromacs job in GPU workstation

Re: [gmx-users] Announcement: new version of GridMAT-MD available

/albert/Desktop/matpack/source/3rdparty/libpng' make[3]: Leaving directory `/home/albert/Desktop/matpack/source/3rdparty/libpng' (cd Matutil ; make ) make[3]: Entering directory `/home/albert/Desktop/matpack/source/Matutil' g++ -ansi -std=c++0x -m64 -DXPM_INCLUDE=X11/xpm.h -c -s -Wall -O3

[gmx-users] how to direct log file correctly?

? Meanwhile tho job won't have any problem going to next step (I am running all the steps in one script). thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org

[gmx-users] new CHARMM-GUI output not supported?

very much best Albert -- 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

[gmx-users] why minimization stop so fast

was spent in domain decomposition, 6 % of the run time was spent in pair search, you might want to increase nstlist (this has no effect on accuracy) gcq#154: Rub It Right Accross Your Eyes (F. Zappa) Thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org

Re: [gmx-users] why minimization stop so fast

Hi Justin: thanks for kind reply. Yes, there many atom clashes in CHARMM-GUI system, so I add very strong force on protein and ligands, and try to minimize the rest of the system do you have any idea how can I solve the issue and make it work? thanks a lot Albert On 04/16/2013 07:09

Re: [gmx-users] why minimization stop so fast

On 04/16/2013 07:28 PM, Justin Lemkul wrote: Create a more physically reasonable starting structure. -Justin the protein and ligand are already minimized, but CHARMM-GUI create the mix lipids automatically which I cannot change them. ALBERT -- gmx-users mailing listgmx-users

Re: [gmx-users] new CHARMM-GUI output not supported?

Hello Mark and Justin: thanks a lot for kind comments. I changed the atom order in forcecfiled .rtp file so that they are the same with the output from CHARMM-GUI, and it works fine now. best Albert On 04/17/2013 12:50 AM, Mark Abraham wrote: Support is not really the right word

Re: [gmx-users] Re: why minimization stop so fast

Hello Brad: thanks for advices. I've also solved the problem after I run the 6.1 minimization step in NAMD. After that, I reimport the lipids system into gromacs, and it no longer complain those issue. best Albert On 04/16/2013 09:59 PM, Brad Van Oosten wrote: Hello,I have had

[gmx-users] why no. of atoms doesn't match?

protein, 1 ligand, 42 chelostrol, 98 POPC and 10079 water molecules. Then I am trying to minimize the system with command: grompp_mpi -f em.mdp -c complex.pdb -o em.tpr However, it always failed with messages: Program grompp_mpi, VERSION 4.6.1 Source code file: /home/albert/Desktop/gromacs

Re: [gmx-users] why no. of atoms doesn't match?

not match topology (topol.top, 51295) It is correct with the topology I defined at the end of topol.top file: [ molecules ] ; Compound#mols Protein 1 LIG1 CHL142 POPC98 SOL10079 thank you very much best Albert On 04/15/2013 07:45 PM, Justin Lemkul wrote: Seriously though

Re: [gmx-users] why no. of atoms doesn't match?

1.00 0.00 MEMB ATOM 6423 H16Y POPA 22 -19.546 21.266 -2.437 1.00 0.00 MEMB ATOM 6424 H16Z POPA 22 -20.104 19.539 -2.286 1.00 0.00 MEMB thank you very much best Albert On 04/15/2013 08:03 PM, Albert wrote: Hello Justin and bv08ay: thanks a lot for kind

[gmx-users] new CHARMM-GUI output not supported?

very much best Albert ---BeginMessage--- Hello: I obtained a POPC lipids from CHARMM-GUI and I found the initial 12 line are following: following atom name order: ATOM 6315 N POPC 22 3.580 -22.614 19.970 1.00-19.29 MEMB ATOM 6316 C12 POPC 22 4.563 -22.414

[gmx-users] shall we add ions in FEP?

? THX Albert -- 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

[gmx-users] how to extract last frame?

Hello: I am trying to extract last frame of my MD simulations with command: trjconv_mpi -f s.xtc -s P-in.gro -dump -1 -o p-out.pdb but it said: WARNING no output, last frame read at t=751.4 gcq#286: Oh, There Goes Gravity (Eminem) thank you very much best Albert -- gmx-users mailing list

[gmx-users] can we use GPU from another machine for calculation?

Hello: I've got two GPU workstation both of which have two GTX690 GPU. Now I am planning to run Gromacs GPU version and I am just wondering can we submit a single GPU jobs in one machine and evoke all GPU resources from both machine? thank you very much best Albert -- gmx-users mailing

Re: [gmx-users] fail to pull

this is too short for whole protein as COM? thank you very much best Albert -- 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

Re: [gmx-users] fail to pull

md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr for pulling .tpr generating. May I ask whey shall we use option -t npt.cpt in this step? Usually we only need to specify .mdp, .gro and .top file for .tpr file thank you very much best Albert On 04/07/2013 05:31

Re: [gmx-users] fail to pull

IC. thanks a lot for explanations. Albert On 04/07/2013 06:08 PM, Justin Lemkul wrote: I'm assuming you're getting that line from my tutorial. You pass the .cpt file to grompp to preserve velocities from the previous equilibration phase. If you don't, what was the point of equilibrating

[gmx-users] where is gromos54a7_lipid FF?

Hello: I saw lots of people is using gromos54a7_lipid FF and I search the gromacs webiste, but didn't find it. Would anybody tell me where can we obtain it? THX Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search

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