Re: [gmx-users] Diffusion/PBC
Hi Debashis, Makes sure that the anion and receptor are together in the reference structure you use for trjconv -pbc nojump Cheers, Tsjerk On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu debashis.sah...@gmail.comwrote: Dear All, I have an problem related to jumping trajectory. In my MD run, there is a receptor molecule which is binding with an halogen anion in water solvent. In the original trajectory, the binding between them looks fine but jumping present. To remove the jumping of the system from trajectory, I have used 'nojump' as discussed in the forum. Now I got a jump-free trajectory, but due to the diffusion here, I have observed that the anion and the receptor are far away from each other. I could not fix the problem. can any one suggest me? Thanks in advance. with regards, *Debashis Sahu* *Central Salt and Marine Chemical Research Institute* *Bhavnagar, Gujarat* *India, 364002.* -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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: Using mpirun on CentOS 6.0
Hi, I am getting the following error while using the command - [root@localhost INGT]# mpirun -np 24 mdrun_mpi -v -deffnm npt Error - /usr/bin/mpdroot: open failed for root's mpd conf filempiexec_localhost.localdomain (__init__ 1208): forked process failed; status=255 I complied gromacs using - ./configure --enable-shared --enable-mpi. I have installed the mpich package , this is what I get when I check for mpirun and mpiexec - [root@localhost /]# which mpirun /usr/bin/mpirun [root@localhost /]# which mpiexec /usr/bin/mpiexec What could be the problem here ?? Thanks 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] free energy
Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. Best Regards Kiana -- 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] extra gro file generation
Dear all, I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Best regards, Sarah Keshavarz -- 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] extra gro file generation
Dear Sarah, you have to use the trjconv command with the flags -b -e and -sep. For example: trjconv -f xxx.trr -s xxx.tpr -o out.gro -b (initial frame to read in ps) -e (last frame to read in ps) -sep Regards El mar, 05-11-2013 a las 01:04 -0800, sarah k escribió: Dear all, I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Best regards, Sarah Keshavarz -- 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] choosing force field
Just out of curiosity -why can you only choose between GROMOS force fields? 2013/11/5 pratibha kapoor kapoorpratib...@gmail.com Dear all I would like to carry out unfolding simulations of my dimeric protein and would like to know which is the better force field to work with out of gromos 96 43 or 53? Also, is gromos 96 43a1 force field redundant? When I searched the previous archive, I could see similar question was raised for gromos 96 43a3 ff and could make out that 53a6 53a7..have entirely different approach in parameterization compared to 43a3 ff. Also 43a3 would give more stable structures. So is the case with my simulations but with force field 43a1 (instead of 43a3). I could see an extra non native helix when I carried out simulations with ff 43a1 which is not present with 53a7 ff. I have no experimental data/re-sources to confirm this. Also simulations on my system has not been done before. I would like to know which out of the two simulations should I consider more reliable-43a1 or 53a7? 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 -- 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] Gromacs-4.6 on two Titans GPUs
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! 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 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] Energy minimization has stopped....
Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: The Feeling of Power was Intoxicating, Magic (Frida Hyvonen) -- Kalyanashis Jana email: kalyan.chem...@gmail.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
Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
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 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] extra gro file generation
On 05.11.2013 10:04, sarah k wrote: I'm going to perform a molecular dynamics simulation on a protein. As a default the simulation gives one final *.gro file. I need to get a .gro file after each say 500 ps of my simulation, in addition of the final file. How can I do so? Riccardo already gave the important hints in another posting, here are some additional explanations. # first, generate an empty subdirectory in order to keep # the simulation directory clean. The rm command is # important if you repeat these steps $ mkdir -p GRO/ ; rm -rf GRO/*.gro # then, decide which part of the system you need: # 0 - evgerything # 1 - the protein # 2 - the cofactor (if any) # Remember: these numbers correspond to the order of molecules # named in the .top-file. If your protein is 1 and you # need only that, do a echo 1 | trjconv -b 500 -noh -novel -skip 2 -sep -nzero 5 -o GRO/out.gro # this will dump the system part 1 (the protein or whatever), # starting from 500 ps (-b) and saving every 2'nd trajectory snapshot. For each option to trjconv (-noh, -novel), please read the manual (where all of this can be found). Regards M. -- 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] Gromacs-4.6 on two Titans GPUs
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) 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 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/
Re: [gmx-users] Energy minimization has stopped....
What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching the Fmax cutoff. 2 is a large number of steps. Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: The Feeling of Power was Intoxicating, Magic (Frida Hyvonen) -- Kalyanashis Jana email: kalyan.chem...@gmail.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] Energy minimization has stopped....
On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -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] free energy
On 11/5/13 3:45 AM, kiana moghaddam wrote: Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. An identical question was asked on the list last week, including responses about external software that will do these calculations. Gromacs does not do MM/PBSA, but other programs will. -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] Re: Energy minimization has stopped....
I have given my .mdp file, ; title = trp_drg warning = 10 cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000.0 ps. nstcomm = 100 nstxout = 250 ; ouput coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 100 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temparature coupling is on Tcoupl = berendsen tau_t = 1.01.0-0.1 1.0 1.0 tc_grps = SOLNA protein OMP CL ref_t = 300300300 300 300 ; Pressure coupling is on pcoupl = berendsen ; Use Parrinello-Rahman for research work pcoupltype = isotropic ; Use semiisotropic when working with membranes tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 And It is a large protein system containing drug molecule and the atoms of whole system is near about 16000. As I did not get any .gro file, thus the MD run was not properly finished. Please suggest me the probable source this kind error. Thank you so much.. On Tue, Nov 5, 2013 at 5:29 PM, jkrie...@mrc-lmb.cam.ac.uk [via GROMACS] ml-node+s5086n5012256...@n6.nabble.com wrote: What does your curve look like? What parameters are you using in the mdp? How big is your system and what kind of molecules are in there? Providing this kind of information would help people work out what the problem is. Then again it may be ok that the minimisation has converged without reaching the Fmax cutoff. 2 is a large number of steps. Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 gcq#322: The Feeling of Power was Intoxicating, Magic (Frida Hyvonen) -- Kalyanashis Jana email: [hidden email]http://user/SendEmail.jtp?type=nodenode=5012256i=0 -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012256i=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=5012256i=2. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list[hidden email]http://user/SendEmail.jtp?type=nodenode=5012256i=3 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=5012256i=4. * 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/Energy-minimization-has-stopped-tp5012252p5012256.html To start a new topic under GROMACS Users Forum, email ml-node+s5086n4370410...@n6.nabble.com To unsubscribe from GROMACS, click
Re: [gmx-users] Energy minimization has stopped....
Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -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 -- Kalyanashis Jana email: kalyan.chem...@gmail.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
Re: [gmx-users] Re: Energy minimization has stopped....
On 11/5/13 7:19 AM, Kalyanashis wrote: I have given my .mdp file, ; title = trp_drg warning = 10 cpp = /usr/bin/cpp define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000.0 ps. nstcomm = 100 nstxout = 250 ; ouput coordinates every 0.5 ps nstvout = 1000 ; output velocities every 2.0 ps nstfout = 0 nstlog = 100 nstenergy = 100 nstlist = 100 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb= 1.0 vdwtype = cut-off rvdw= 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Berendsen temparature coupling is on Tcoupl = berendsen tau_t = 1.01.0-0.1 1.0 1.0 tc_grps = SOLNA protein OMP CL ref_t = 300300300 300 300 These settings make no sense. Please read http://www.gromacs.org/Documentation/Terminology/Thermostats. ; Pressure coupling is on pcoupl = berendsen ; Use Parrinello-Rahman for research work pcoupltype = isotropic ; Use semiisotropic when working with membranes tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord-scaling= all ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 And It is a large protein system containing drug molecule and the atoms of whole system is near about 16000. As I did not get any .gro file, thus the MD run was not properly finished. Please suggest me the probable source this kind error. The run crashes because your energy minimization effectively failed. -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] Energy minimization has stopped....
On 11/5/13 7:31 AM, Kalyanashis Jana wrote: Dear Justin, Can you please tell me, how I can solve this problem?? If I will change the coordinate of atom 15461, will it help me? But you know, I did this step changing the position of drug molecule and I got same error. You should first do what I suggested before. The reason for a large force is either (1) bad atomic clashes that should be apparent upon visual inspection or (2) bad topology for the drug. -Justin On Tue, Nov 5, 2013 at 5:44 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 6:28 AM, Kalyanashis Jana wrote: Hi, Whenever I am trying to do position retrained MD run, It has been stopped at middle of the MD run. I have given the following error. Can you please suggest me something to resolve this error? Energy minimization has stopped, but the forces havenot converged to the requested precision Fmax 100 (whichmay not be possible for your system). It stoppedbecause the algorithm tried to make a new step whose sizewas too small, or there was no change in the energy sincelast step. Either way, we regard the minimization asconverged to within the available machine precision,given your starting configuration and EM parameters. Double precision normally gives you higher accuracy, butthis is often not needed for preparing to run moleculardynamics. writing lowest energy coordinates. Steepest Descents converged to machine precision in 20514 steps, but did not reach the requested Fmax 100. Potential Energy = -9.9811250e+06 Maximum force = 6.1228135e+03 on atom 15461 Norm of force = 1.4393512e+01 Visualize the output, specifically near atom 15461. The forces there are too high and cannot be resolved further. Any attempt to use these coordinates for dynamics will probably lead to a crash. -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 -- == 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] mdrun
Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd way (strange extensions) e.g em.gro.tprr or md.tpr.cpt, md.tpr.xtc. Can anyone explain the cause of 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
Re: [gmx-users] mdrun
On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd way (strange extensions) e.g em.gro.tprr or md.tpr.cpt, md.tpr.xtc. Can anyone explain the cause of this? You are issuing the command in a way that you probably don't want. I suspect what you are doing is: mdrun -deffnm md.tpr The -deffnm option is for the base file name and should not include an extension. mdrun is only doing what you tell it; you're saying, all my files are named md.tpr, and you can put whatever the necessary extension is on them. What you want is: mdrun -deffnm md -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] free energy
Dear Kiana, You can contact with Paissoni Cristina (email: paissoni.crist...@hsr.it) to get tool using MM/PBSA with GROMACS. Hope it help :) Cheers, Kieu Thu On Tue, Nov 5, 2013 at 7:18 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 3:45 AM, kiana moghaddam wrote: Dear GMX Users I am using parmbsc0 force field to study DNA-ligand interaction but my problem is free energy calculation (MMPBSA) for this interaction. How can I calculate free energy using MMPBSA approach? Thank you very much for your time and consideration. An identical question was asked on the list last week, including responses about external software that will do these calculations. Gromacs does not do MM/PBSA, but other programs will. -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] mdrun
Dear Dr Justin, Much appreciation. You nailed it. Kind regards. On Tue, Nov 5, 2013 at 2:41 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/5/13 7:37 AM, MUSYOKA THOMMAS wrote: Dear Users, I am running MD simulations of a protein-ligand system. Sometimes when i do an mdrun, be it for the energy minimization or during the nvt and npt equillibration or the actual md run step, sometimes the output files are named in a very odd way (strange extensions) e.g em.gro.tprr or md.tpr.cpt, md.tpr.xtc. Can anyone explain the cause of this? You are issuing the command in a way that you probably don't want. I suspect what you are doing is: mdrun -deffnm md.tpr The -deffnm option is for the base file name and should not include an extension. mdrun is only doing what you tell it; you're saying, all my files are named md.tpr, and you can put whatever the necessary extension is on them. What you want is: mdrun -deffnm md -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 -- *MUSYOKA THOMMAS MUTEMIMob nos **+27844846540* *B.Sc Biochemistry (Kenyatta University),MSc Pharmaceutical Science (Nagasaki University)* *PhD Student-Bioinformatics (Rhodes University)*Skype ID- MUSYOKA THOMMAS MUTEMI Alternative email - thom...@sia.co.ke *Do all the good you can, By all the means you can, In all the ways you can, In all the places you can,At all the times you can,To all the people you can,As long as ever you can. - John Wesley. * -- 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] CHARMM .mdp settings for GPU
Dear All, I intend to run a membrane-protein system in GPU. I am slightly confused about the .mdp settings Non-gpu settings (according to original CHARMM FF paper): 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 For cutoff-scheme = Verlet , shouldn't rvdw=rcoulomb? How should the above settings be modified? Thank you. -- 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
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
[gmx-users] Re: Replacing atom
Hi, I need to replace an atom with another in the considered system. I'd like to know if it is possible and if so what changes I need to do. thanks j.rahrow On Thu, Oct 31, 2013 at 12:47 PM, J Alizadeh j.alizade...@gmail.com wrote: Hi, I need to replace an atom with another in the considered system. I'd like to know if it is possible and if so what changes I need to do. thanks j.rahrow -- 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?
29420 Atoms with a some tuning of the write out and communication intervals: nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites 1 node 212 ns/day 2 nodes 295 ns/day -- 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] extra gro file generation
Dear Riccardo Concu and Mirco Wahab, Thanks for your perfect responses. Regards, Sarah -- 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: Replacing atom
On 11/5/13 10:34 AM, J Alizadeh wrote: Hi, I need to replace an atom with another in the considered system. I'd like to know if it is possible and if so what changes I need to do. The coordinate file replacement is trivial. Just open the file in a text editor and repname the atom. The topology is trickier, because you need a whole new set of parameters. -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] Gentle heating with implicit solvent
I wonder whether increasing the surface tension parameter sa-surface-tension might solve the problem with the protein unfolding. Thanks, Gianluca On Mon, 4 Nov 2013, Gianluca Interlandi wrote: Hi Justin, We are using infinite cutoffs (all vs all). Here is the mdp file for the heating (please note that -DPOSRES is commented out) and the time step is 1 fs: ; VARIOUS PREPROCESSING OPTIONS = title= cpp = /lib/cpp include = ;define = -DPOSRES ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit= 0 dt = 0.001 nsteps = 20 ; mode for center of mass motion removal = comm-mode= Linear ; number of steps for center of mass motion removal = nstcomm = 1 ; group(s) for center of mass motion removal = comm-grps= ; LANGEVIN DYNAMICS OPTIONS = ; Temperature, friction coefficient (amu/ps) and random seed = ;bd-temp = 300 bd-fric = 0 ld_seed = 1993 ; IMPLICIT SOLVENT OPTIONS = implicit-solvent = GBSA gb-algorithm = OBC rgbradii = 0 ; ENERGY MINIMIZATION OPTIONS = ; Force tolerance and initial step-size = emtol= 0.01 emstep = 0.01 ; Max number of iterations in relax_shells = niter= 100 ; Step size (1/ps^2) for minimization of flexible constraints = fcstep = 0 ; Frequency of steepest descents steps when doing CG = nstcgsteep = 1000 ; 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 = 100 nstenergy= 100 ; Output frequency and precision for xtc file = nstxtcout= 1000 xtc_precision= 1000 ; This selects the subset of atoms for the xtc file. You can = ; select multiple groups. By default all atoms will be written. = xtc-grps = ; Selection of energy groups = energygrps = ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 0 ; ns algorithm (simple or grid) = ns_type = simple ; Periodic boundary conditions: xyz or no = pbc = no ; nblist cut-off = rlist= 0 ;rlistlong= 1.8 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = Cut-off rcoulomb_switch = 0 rcoulomb = 0 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r= 1 ; Method for doing Van der Waals = vdw-type = Cut-off ; cut-off lengths= rvdw_switch = 0 rvdw = 0 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; 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= 4 ewald_rtol = 1e-05 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = Tcoupl = V-rescale ; Groups to couple separately = tc_grps = Protein ; Time constant (ps) and reference temperature (K) = tau_t= 0.1 ref_t= 300 ; Pressure coupling = Pcoupl = no Pcoupltype = isotropic refcoord_scaling = All ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p= 1.0 compressibility = 4.5e-5 ref_p= 1.0 ; SIMULATED ANNEALING CONTROL = annealing= single ; Number of time points to use for specifying annealing in each group annealing_npoints = 21 ; List of times at the annealing points for each group annealing_time= 0 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 ; Temp. at each annealing point, for each group annealing_temp= 5 30 30 60 60 90 90 120 120 150 150 180 180 210 210 240 240 270 270 300 300 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = yes gen_temp = 5 gen_seed = 173529 ; OPTIONS FOR BONDS = constraints = none ; Type of constraint algorithm = ;constraint_algorithm = Lincs ; Do not constrain the start configuration = unconstrained_start = no ; Use successive overrelaxation to
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?
Timo, Have you used the default settings, that is one rank/GPU? If that is the case, you may want to try using multiple ranks per GPU, this can often help when you have 4-6 cores/GPU. Separate PME ranks are not switched on by default with GPUs, have you tried using any? Cheers, -- Szilárd Páll On Tue, Nov 5, 2013 at 3:29 PM, Timo Graen tgr...@gwdg.de wrote: 29420 Atoms with a some tuning of the write out and communication intervals: nodes again: 2 x Xeon E5-2680v2 + 2 x NVIDIA K20X GPGPUs @ 4fs vsites 1 node 212 ns/day 2 nodes 295 ns/day -- 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: Gromacs-4.6 on two Titans GPUs
Hi Mike, I have similar configurations except a cluster of AMD-based linux platforms with 2 GPU cards. Your suggestion works. However, the performance of 2 GPU discourages me because , for example, with 1 GPU, our computer node can easily obtain a simulation of 31ns/day for a protein of 300 amino acids but with 2 GPUs, it goes as far as 38 ns/day. I am very curious as to why the performance of 2 GPUs is under expectation. Is there any overhead that we should pay attention to ? Note that these 2GPU cards are linked by a SLI bridge within the same node. Since the computer nodes of our cluster have at least one GPU but they are connected by slow network cards ( 1GB/sec), unfortunately, I reasonably doubt that the performance will not be proportional to the total number of GPU cards. I am wondering if you have any suggestion about a cluster of GPU nodes. For example, will a infiniband networking help increase a final performance when we execute a mpi task ? or what else ? or forget about mpi and use single GPU instead. Any suggestion is highly appreciated. Thanks. Dwey Date: Tue, 5 Nov 2013 16:20:39 +0100 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] Gromacs-4.6 on two Titans GPUs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: camnumasm5ht40ub+unppv7gmhqzxsb6psewma+hblv+gnb2...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 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
[gmx-users] Re: Hardware for best gromacs performance?
Hi Timo, Can you provide a benchmark with 1 Xeon E5-2680 with 1 Nvidia k20x GPGPU on the same test of 29420 atoms ? Are these two GPU cards (within the same node) connected by a SLI (Scalable Link Interface) ? Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012276.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
Re: [gmx-users] Re: Gromacs-4.6 on two Titans GPUs
Hi Dwey, First and foremost, make sure to read the http://www.gromacs.org/Documentation/Acceleration_and_parallelization page, in particular the Multiple MPI ranks per GPU section which applies in your case. Secondly, please do post log files (pastebin is your friend), the performance table at the end of the log tells much the performance story and based on that I/we can make suggestions. Using multiple GPU requires domain-decomposition which does have a considerable overhead, especially comparing no DD with DD (i.e. 1 GPU run with 2 GPU run). 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. 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). Cheers, -- Szilárd On Tue, Nov 5, 2013 at 9:29 PM, Dwey mpi...@gmail.com wrote: Hi Mike, I have similar configurations except a cluster of AMD-based linux platforms with 2 GPU cards. Your suggestion works. However, the performance of 2 GPU discourages me because , for example, with 1 GPU, our computer node can easily obtain a simulation of 31ns/day for a protein of 300 amino acids but with 2 GPUs, it goes as far as 38 ns/day. I am very curious as to why the performance of 2 GPUs is under expectation. Is there any overhead that we should pay attention to ? Note that these 2GPU cards are linked by a SLI bridge within the same node. Since the computer nodes of our cluster have at least one GPU but they are connected by slow network cards ( 1GB/sec), unfortunately, I reasonably doubt that the performance will not be proportional to the total number of GPU cards. I am wondering if you have any suggestion about a cluster of GPU nodes. For example, will a infiniband networking help increase a final performance when we execute a mpi task ? or what else ? or forget about mpi and use single GPU instead. Any suggestion is highly appreciated. Thanks. Dwey Date: Tue, 5 Nov 2013 16:20:39 +0100 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] Gromacs-4.6 on two Titans GPUs To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: camnumasm5ht40ub+unppv7gmhqzxsb6psewma+hblv+gnb2...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 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
Re: [gmx-users] Re: Hardware for best gromacs performance?
On Tue, Nov 5, 2013 at 9:55 PM, Dwey Kauffman mpi...@gmail.com wrote: Hi Timo, Can you provide a benchmark with 1 Xeon E5-2680 with 1 Nvidia k20x GPGPU on the same test of 29420 atoms ? Are these two GPU cards (within the same node) connected by a SLI (Scalable Link Interface) ? Note that SLI has no use for compute, only for graphics. -- Szilárd Thanks, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012276.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] Re: Gromacs-4.6 on two Titans GPUs
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 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] Re: Hardware for best gromacs performance?
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
RE: [gmx-users] RE: Gibbs Energy Calculation and charges
Thank you for the pointer Michael. couple-intramol = no What a diff of the output from gmxdump of the two tpr files shows is in both of these cases (normal and double charged), when: lambda is set to 1.0 (atoms within both molecules will have zero charge) lambda is set to 0.00 and 0.50, respectively (both will have the same charge) There are the following differences: functype[] = LJC14_Q, qi and qj are set to the original charges, not the ones scaled by lambda functype[] = LJC_NB, qi and qj are set to the original charges, not the ones scaled by lambda atom[] = q is set to the original charges, not the ones scaled by lambda So this explains why I do not see the two topologies giving the same value at the same atomic charges, since the topologies being simulated are not the same. The 1-4 charge interactions are still at the original charges, as are the 1-5 and beyond. What is the reason that the charges are being left untouched here with changing lambda? I can understand when we are dealing with LJ/van der Waals, since the 1-4 are important for the proper dihedrals, but what is the reason for charges being left untouched? Having thought this through, answered it myself, it is because here we are interested in molecule - external environment interactions being turned off, we are moving the entire molecule from full interacting with its external environment to non-interacting. The molecule itself should be left alone. Turning to the side issue of turning couple-intramol on - couple-intramol = yes diff of the equivalent files, there are the following differences: functype[] = LJC14_Q, qi and qj are set to the original charges, not the ones scaled by lambda atom[] = q is set to the original charges, not the ones scaled by lambda Which confirms what Michael mentioned earlier about couple-intramol only affecting those 1-5 and beyond i.e. LJC_NB Which then begs the question, why does the value of dH/dl change so dramatically when this option is turned on, as I observed at http://ozreef.org/stuff/gromacs/couple-intramol.png The only thing being changed is the fact that LJC_NB is now being scaled with lambda. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Michael Shirts Sent: Thursday, 31 October 2013 1:52 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] RE: Gibbs Energy Calculation and charges I likely won't have much time to look at it tonight, but you can see exactly what the option is doing to the topology. run gmxdump on the tpr. All of the stuff that couple-intramol does is in grompp, so the results will show up in the detailed listings of the interactions, and which ones have which values set for the A and B states. On Wed, Oct 30, 2013 at 5:36 PM, Dallas Warren dallas.war...@monash.edu wrote: Michael, thanks for taking the time to comment and have a look. The real issue I am having is a bit deeper into the topic than that, my last reply was just an observation on something else. Will summarise what I have been doing etc. I have a molecule that are calculating the Gibbs energy of hydration and solvation (octanol). In a second topology the only difference is that the atomic charges have been doubled. Considering that charges are scaled linearly with lambda, the normal charge values of dH/dl from lambda 0 to 1 obtained should reproduce that of the double charged molecule from lambda 0.5 to 1.0. Is that a correct interpretation? Since the only difference should be that charge of the atoms and over that range the charge will be identical. I was using couple-intramol = no and the following are the results from those simulations. For the OE atom within the molecule, I have plotted the following graphs of dH/dl versus charge of that atom for both of the topologies. octanol - http://ozreef.org/stuff/octanol.gif water - http://ozreef.org/stuff/water.gif mdp file - http://ozreef.org/stuff/gromacs/mdout.mdp The mismatch between the two topologies is the real issue that I am having. I was hoping to get the two to overlap. My conclusion based on this is that there is actually something else being changed with the topology by GROMACS when the simulations are being run. The comments in the manual allude to that, but not entirely sure what is going on. From the manual: couple-intramol: no All intra-molecular non-bonded interactions for moleculetype couple-moltype are replaced by
[gmx-users] RE: Gibbs Energy Calculation and charges
Thanks for the suggestion Chris. Had a quick look and can't see easily how to do this, but I think I am at a point now where it is not an issue and don't have to actually do this. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. -Original Message- From: gmx-users-boun...@gromacs.org [mailto:gmx-users- boun...@gromacs.org] On Behalf Of Christopher Neale Sent: Saturday, 2 November 2013 3:50 AM To: gmx-users@gromacs.org Subject: [gmx-users] Gibbs Energy Calculation and charges Dear Dallas: Seems like you could test Michael's idea by removing all 1-4 NB interactions from your topology. It won't produce any biologically useful results, but might be a worthwhile check to see if indeed this is the issue. To do this, I figure you would set gen-pairs to no in the [ defaults ] directive of forcefield.itp, remove the [ pairtypes ] section from ffnonbonded.itp, and remove the [ pairs ] section from your molecular .itp file. (You can quickly check that the 1-4 energy is zero in all states to ensure that this works). If that gives you the result that you expect, then you could go on to explicitely state the 1-4 interactions for the A and B states (I presume that this is possible). Of course, you should be able to jump directly to this second test, but the first test might be useful because it rules out the possibility that you make a typo somewhere. Chris. -- original message -- I think the grammar got a little garbled there, so I'm not sure quite what you are claiming. One important thing to remember; 1-4 interactions are treated as bonded interactions right now FOR COUPLE intramol (not for lambda dependence of the potential energy function), so whether couple-intramol is set to yes or no does not affect these interactions at all. It only affects the nonbondeds with distances greater than 1-5. At least to me, this is nonintuitive (and we're coming up with a better scheme for 5.0), but might that explain what you are getting? On Tue, Oct 29, 2013 at 9:44 PM, Dallas Warren Dallas.Warren at monash.edu wrote: Just want this to make another pass, just in case those in the know missed it. Using couple-intrmol = yes the resulting dH/dl plot actually looks like that at lamba = 1 it is actually equal to couple-intramol = no with lambda = 0. Should that be the case? Catch ya, Dr. Dallas Warren -- 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-users Digest, Vol 115, Issue 16
Message: 5 Date: Mon, 04 Nov 2013 13:32:52 -0500 From: Justin Lemkul jalem...@vt.edu Subject: Re: [gmx-users] Analysis tools and triclinic boxes To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: 5277e854.9000...@vt.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Justin, Thanks for the response. My question was prompted by line 243 in gmx_cluster.c which states /* Should use pbc_dx when analysing multiple molecueles,but the box is not stored for every frame.*/ I just wanted to verify that analysis tools are written for any box shape. Cheers, Stephanie On 11/4/13 1:29 PM, Stephanie Teich-McGoldrick 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. All analysis tools should work correctly for all box types. Is there a specific issue you are having, or just speculation? -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 == On Mon, Nov 4, 2013 at 12:28 PM, gmx-users-requ...@gromacs.org wrote: Send gmx-users mailing list submissions to gmx-users@gromacs.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.gromacs.org/mailman/listinfo/gmx-users or, via email, send a message with subject or body 'help' to gmx-users-requ...@gromacs.org You can reach the person managing the list at gmx-users-ow...@gromacs.org When replying, please edit your Subject line so it is more specific than Re: Contents of gmx-users digest... Today's Topics: 1. Re: Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0 (Mark Abraham) 2. Analysis tools and triclinic boxes (Stephanie Teich-McGoldrick) 3. Group protein not found in indexfile (Steve Seibold) 4. Re: Group protein not found in indexfile (Justin Lemkul) 5. Re: Analysis tools and triclinic boxes (Justin Lemkul) 6. Re: TFE-water simulation (Archana Sonawani-Jagtap) 7. Re: Gentle heating with implicit solvent (Gianluca Interlandi) -- Message: 1 Date: Mon, 4 Nov 2013 17:05:36 +0100 From: Mark Abraham mark.j.abra...@gmail.com Subject: Re: [gmx-users] Re: Installation Gromacs 4.5.7 on rocluster cluster with centos 6.0 To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: CAMNuMAQcWLcKA=GPG1Ewr8s4A=PoTGOSWaqa= s_uzbyw8uf...@mail.gmail.com Content-Type: text/plain; charset=ISO-8859-1 On Mon, Nov 4, 2013 at 12:01 PM, bharat gupta bharat.85.m...@gmail.com wrote: 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
[gmx-users] Re: Hardware for best gromacs performance?
Hi Szilárd and all, Thanks very much for the information. I am more interested in getting single simulations to go as fast as possible (within reason!) rather than overall throughput. Would you expect that the more expensive dual Xeon/Titan systems would perform better in this respect? Cheers David -- View this message in context: http://gromacs.5086.x6.nabble.com/Hardware-for-best-gromacs-performance-tp5012124p5012283.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
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] Diffusion/PBC
Your best bet is probably to center everything on the receptor. That will prevent jumping of the receptor only, which is hopefully all you need. -Trayder On Tue, Nov 5, 2013 at 7:14 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Debashis, Makes sure that the anion and receptor are together in the reference structure you use for trjconv -pbc nojump Cheers, Tsjerk On Tue, Nov 5, 2013 at 8:12 AM, Debashis Sahu debashis.sah...@gmail.com wrote: Dear All, I have an problem related to jumping trajectory. In my MD run, there is a receptor molecule which is binding with an halogen anion in water solvent. In the original trajectory, the binding between them looks fine but jumping present. To remove the jumping of the system from trajectory, I have used 'nojump' as discussed in the forum. Now I got a jump-free trajectory, but due to the diffusion here, I have observed that the anion and the receptor are far away from each other. I could not fix the problem. can any one suggest me? Thanks in advance. with regards, *Debashis Sahu* *Central Salt and Marine Chemical Research Institute* *Bhavnagar, Gujarat* *India, 364002.* -- 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 -- Tsjerk A. Wassenaar, Ph.D. -- 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_lie and ligand only simulation
Dear users, When the simulation was carried out with PME rcoulomb was set equal to rlist. But when I need to to ligand-water simulation without PME (with RF-0) then it requires rlist greater by 0.1-0.3 than rcoulomb. So if I rerun protein-ligand-water simulation there could be more differences in the energies isnt it? Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:51 PM, Kavyashree M hmkv...@gmail.com wrote: Ok thank you. I thought it was for protein-ligand-water that needs to be rerun without PME. Thanks Regards Kavya On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 12:14 PM, Kavyashree M wrote: Sir, Thank you. Should the ligand-water MD be done without PME? I already answered this. Please read my previous reply again. -Justin Thank you Regards Kavya On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/2/13 1:22 AM, Kavyashree M wrote: Dear Users, Its mentioned in the list that it would be wrong to use g_lie on a simulation which uses PME. So kindly suggest any other way available to get the free energy of ligand binding other using g_lie? The original simulation should be done with PME, then the energies recalculated using mdrun -rerun without PME. More detailed methods are available in the list archive; this topic gets discussed a lot. -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 -- == 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
