[gmx-users] How to simulate pure methane system?
Hello all, Now I want to have a simulation of water and methane system, but when I wrote a methane.itp and the force field file, it could not run correctly. I used tip4p water and the opls-aa methane. According to the simulation with NPT, not only the pure methane system, but also the water and methane system, the simulated box became larger and lager, I don't know why and I cann't find the problem, could you tell me what's the problem? looking forward to your reply and thanks a lot. Liu Chanjuan Institute of Geology and Geophysics, Chinese Academy of Sciences TEL:010-82998424 E-mail:chanjuan0...@126.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] retraining multiple protein ligand interactions using pull-code
Hello everyone, I am new to using gromacs. I am currently studying an enzyme catalysing a transfer reaction. there are two substrates and I want to restraint specific interactions between different parts of the ligands and the protein. As I understand so far from reading various discussions in the group, restraining such interactions is possible through pull code, But we can assign only one pull group0, I am wondering if there is better way to restraint multiple interactions between multiple molecules in a single simulation. If not through pull-code, what will be the best way to ensure many specific intermolecular restraints? thank you very much in advance. regards, Saravanan -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] no CUDA-capable device is detected
Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This worked in my system (MacOS/Darwin). Just make sure to set the variables CC and CXX to point to the right compiler version when you run cmake. George Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| | 0 Not Supported | +-+ What am I missing that Gromacs is not detecting the GPUs. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] no CUDA-capable device is detected
Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This worked in my system (MacOS/Darwin). Just make sure to set the variables CC and CXX to point to the right compiler version when you run cmake. George Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| | 0 Not Supported | +-+ What am I missing that Gromacs is not detecting the GPUs. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] bond conversion between charmm and g96
p{margin:0;padding:0;} Dear Justin, Thank for your pointing out my issues. I just want to know how it can be converted. I have referred the equation in chapter 4 and do not know exactly how I use them. For example, The C-O bond distance and force constant written as (0.112 and 3.7000e+07 ) in gromos, whereas in charmm27 written as ( 0.1128 and 933032.0). I found the equation for g96 type covalent potential Vb (rij) and force constant Fi(rij) and don't know how do i use this for above purpose? Could you elaborate an example how it can be done? Thanks a lot. Thanks for the mail justin. In charmm27.ff, the value for bonded are in b0 and ko format, whereas the gromos uses them in different way? If so, how do i convert between them? Please consult the manual, Chapters 4 and 5 for all the relevant equations and implementation. The value i incorporated for specific atoms are from published journals. Thanks in advance. I think you're missing my point though. Just because something is published, doesn't mean you can use it for whatever purpose you like. People spend years working out properly balanced force fields, and if you try to put in some new atom type, it upsets the balance of every interaction. You may be OK within the context of CHARMM (depending on what the paper is, and what parameter set they modified), but I can guarantee you that if you're trying to incorporate CHARMM parameters into GROMOS, all you're doing is producing a pile of trash. You can probably make it work from a topology standpoint, but you shouldn't be doing it. I hope my perspective is clear; I'm trying to save you from wasted effort. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] no CUDA-capable device is detected
On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). There is an work around with gcc 4.7.2. Please see http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This worked in my system (MacOS/Darwin). Just make sure to set the variables CC and CXX to point to the right compiler version when you run cmake. George Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| | 0 Not Supported | +-+ What am I missing that Gromacs is not detecting the GPUs. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org.
RE: [gmx-users] no CUDA-capable device is detected
Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). There is an work around with gcc 4.7.2. Please see http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This worked in my system (MacOS/Darwin). Just make sure to set the variables CC and CXX to point to the right compiler version when you run cmake. George Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| | 0 Not Supported | +-+ What am I missing that Gromacs is not detecting the GPUs. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the
[gmx-users] Re: diffusion constant level off
Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 I have strange Diffusion results (especially 10,50,100,150,200 ns). How can I fix this problem? Results: Time (ns) D(cm^2/s) 10 0.1616 20 0.0735 30 0.0775 40 0.1097 50 0.1471 60 0.0468 70 0.0667 80 0.0727 90 0.0664 100 0.1336 110 0.0899 120 0.0572 130 0.0506 140 0.0723 150 0.1466 160 0.0703 170 0.081 180 0.0278 190 0.1121 200 0.3136 2013/3/27 Ahmet yıldırım ahmedo...@gmail.com Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? Gromacs manual: -type:Compute diffusion coefficient in one direction:no, x, y or z -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z -ten:Calculate the full tensor 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? 3.) From manual: The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... What is (D*t + c)? What are the meaning of D and c? 4.) What should be Time between restarting points in trajectory? Thanks in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I have strange Diffusion results (especially 10,50,100,150,200 ns). How can I fix this problem? Results: Time (ns) D(cm^2/s) 10 0.1616 20 0.0735 30 0.0775 40 0.1097 50 0.1471 60 0.0468 70 0.0667 80 0.0727 90 0.0664 100 0.1336 110 0.0899 120 0.0572 130 0.0506 140 0.0723 150 0.1466 160 0.0703 170 0.081 180 0.0278 190 0.1121 200 0.3136 2013/3/27 Ahmet yıldırım ahmedo...@gmail.com Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? Gromacs manual: -type:Compute diffusion coefficient in one direction:no, x, y or z -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z -ten:Calculate the full tensor 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? 3.) From manual: The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... What is (D*t + c)? What are the meaning of D and c? 4.) What should be Time between restarting points in trajectory? Thanks in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: Atoms are fused after inserting in membrane
Does that mean the atoms will shrink and adjust at the time inflategro step and this closely packed lipids will stay apart? Because as you said the energy of course will be high on selected atoms during first EM step. Could you suggest me that, can I proceed as such with my system, since there is no problem in grompp and EM step (except high energy on some atom). The energy will normalize during molecular dynamics stage. Dr. Vitaly Chaban or Do I need to manually remove those overlapping lipids and water molecules. Thanks in advance -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] no CUDA-capable device is detected
Hi, If mdrun says that it could not detect GPUs it simply means that the GPU enumeration found no GPUs, otherwise it would have printed what was found. This is rather strange because mdrun uses the same mechanism the deviceQuery SDK example. I really don't have a good idea what could be the issue, but you could try recompiling or compiling with CUDA 4.2 to see if any of that makes a difference. Let us know if you figured out something. Cheers, -- Szilárd On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess g...@hotmail.com wrote: Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). There is an work around with gcc 4.7.2. Please see http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This worked in my system (MacOS/Darwin). Just make sure to set the variables CC and CXX to point to the right compiler version when you run cmake. George Dear GMX Users, I am trying to execute Gromacs 4.6.1 on one of the GPU server: *OS*: OpenSuse 12.3 x86_64 3.7.10-1.1-desktop (Kernel Release) *gcc*: 4.7.2 CUDA Library paths #CUDA-5.0 export CUDA_HOME=/usr/local/cuda-5.0 export PATH=$CUDA_HOME/bin:$PATH export LD_LIBRARY_PATH=$CUDA_HOME/lib64:/lib:$LD_LIBRARY_PATH The gromacs has been compiled with CMAKE_PREFIX_PATH=/opt/apps/fftw-3.3.3/single:/usr/local/cuda-5.0 cmake .. -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/apps/gromacs/461/single -DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_461 -DGMX_LIBS_SUFFIX=_461 -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda *Error on executing mdrun * * * *NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. Will use 24 particle-particle and 8 PME only nodes This is a guess, check the performance at the end of the log file Using 32 MPI threads No GPUs detected *I checked my cuda installation. I am able to compile and execute the sample programmes e.g., deviceQuery. Also executed *nvidia-smi *: +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 49C N/A N/A / N/A | 3% 16MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 30% 38C P8 16W / 225W | 0% 13MB / 5119MB | 0% Default | +---+--+--+ +-+ | Compute
[gmx-users] SMD : pulling both primes of DNA
The easiest solution would be using 'pull_geometry = distance' in all three dimensions. Then you can be sure that both groups are pulled together. Small remark: One group would be fixed for the pulling, and the second group gets pulled towards the first group. So if you want to have both groups really close, this setup would be the easiest solution. If you really to pull both groups to a point in the middle between them, i think you would need 'pull_geometry = position': Use some part of the DNA as the reference group and put the origin of the pulling (via 'pull_init') to the middle point. Then make two pull-groups + 'pull_vec1' or 'pull_vec2', from each DNA part, which you want to pull to the middle point. In principle this setup should work, but you can run into problems if the structure of the DNA changes and the middle point, to where you pull both groups, moves somewhat around. hard to explain... I would stick to the first approach... What pull-mode did you use? You could use 'pull = constraint', measure the distance between both groups and then pull with a given pulling velocity so long till both groups should meet. Since you use a constraint instead of a restraining potential, the groups should be definitly pulled together (or some other parameters in the .mdp file are wrong). Greetings Thomas Am 27.03.2013 20:16, schrieb gmx-users-requ...@gromacs.org: Hello All, My simulation system is composed of DNA and want to pull both of the primes at the same time towards each other. I have tried every possible set of parameters in pull code...and i am not able to pull them together. it's like ... the DNA molecule is aligned along Y-axis and if want to pull both ends at the same time that means pulling in -Y and +Y direction at the same time. if anyone successfully implemented such ...simulations... Please provide me with some idea about this problem. Thank you Raghav -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] no CUDA-capable device is detected
On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, If mdrun says that it could not detect GPUs it simply means that the GPU enumeration found no GPUs, otherwise it would have printed what was found. This is rather strange because mdrun uses the same mechanism the deviceQuery SDK example. I really don't have a good idea what could be the issue, but you could try recompiling or compiling with CUDA 4.2 to see if any of that makes a difference. Let us know if you figured out something. Cheers, Thanks Szilárd for the eye opening comment. I just tried running gromacs as root. I recalled I had executed deviceQuery as root. While executing as user it produces the same error : */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected* Now, running gromacs as root, it is running successfully (I suppose). Output of nvidia-smi +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 50% 62CP0 106W / 225W | 2% 87MB / 5119MB | 76% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | |1 9127 mdrun_461 72MB | +-+ Output of md.log 2 GPUs detected: #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible 1 GPU auto-selected for this run: #0 I think there is something relate to permissions. Though nvcc has 755 permission, something else might require additional permissions. Chandan -- Szilárd On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess g...@hotmail.com wrote: Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA 5.0? In my hands, gcc 4.7.2 could not compile CUDA 5.0 (I think there was some kind of incompatibility between the two). There is an work around with gcc 4.7.2. Please see http://svshift.blogspot.in/2013/03/running-nvidai-cuda-sdk-50-on-opensuse.html Can you try compiling both CUDA 5.0 and GROMACS with gcc 4.6.1? This
Re: [gmx-users] Re: diffusion constant level off
Dear Prof.Spoel, if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I have strange Diffusion results (especially 10,50,100,150,200 ns). How can I fix this problem? Results: Time (ns) D(cm^2/s) 10 0.1616 20 0.0735 30 0.0775 40 0.1097 50 0.1471 60 0.0468 70 0.0667 80 0.0727 90 0.0664 100 0.1336 110 0.0899 120 0.0572 130 0.0506 140 0.0723 150 0.1466 160 0.0703 170 0.081 180 0.0278 190 0.1121 200 0.3136 2013/3/27 Ahmet yıldırım ahmedo...@gmail.com Dear users, I used the following commands to get diffusion constants (every 10 ns) of a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory every 20 ps). I looked at RMSD vs average structure, RMSD vs starting structure, Radius of gyration, RMSD matrix. This simulation has reached to converge at last 50 ns. g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 1 g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 1 -e 2 g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 2 -e 3 ... g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 9 -e 10 1.) I used the above commands without the following flags ( -type, -lateral and -ten). Which diffusion will the above comands give? is it bulk diffusion? Gromacs manual: -type:Compute diffusion coefficient in one direction:no, x, y or z -lateral:Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z -ten:Calculate the full tensor 2.) I plotted diffusions (10 values) as function of time. Diffusions dont converge. Did I do any steps by mistake? 3.) From manual: The diffusion constant is calculated by least squares fitting a straight line (D*t + c)... What is (D*t + c)? What are the meaning of D and c? 4.) What should be Time between restarting points in trajectory? Thanks in advance -- Ahmet Yıldırım -- Ahmet Yıldırım -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] no CUDA-capable device is detected
Hi !! I problem with the permission of /dev/nvidia* changed it to 0666 /dev/nvidia* Everything resolved. mdrun can be executed as normal user. Thanks everyone. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury iitd...@gmail.comwrote: On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.sewrote: Hi, If mdrun says that it could not detect GPUs it simply means that the GPU enumeration found no GPUs, otherwise it would have printed what was found. This is rather strange because mdrun uses the same mechanism the deviceQuery SDK example. I really don't have a good idea what could be the issue, but you could try recompiling or compiling with CUDA 4.2 to see if any of that makes a difference. Let us know if you figured out something. Cheers, Thanks Szilárd for the eye opening comment. I just tried running gromacs as root. I recalled I had executed deviceQuery as root. While executing as user it produces the same error : */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected* Now, running gromacs as root, it is running successfully (I suppose). Output of nvidia-smi +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 50% 62CP0 106W / 225W | 2% 87MB / 5119MB | 76% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | |1 9127 mdrun_461 72MB | +-+ Output of md.log 2 GPUs detected: #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible 1 GPU auto-selected for this run: #0 I think there is something relate to permissions. Though nvcc has 755 permission, something else might require additional permissions. Chandan -- Szilárd On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess g...@hotmail.com wrote: Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue. I guess mdrun picked up GPU 0, which it should have ignored. You only want to use GPU 1. Could you try running: mdrun -ntmpi 1 -gpu_id 1 $mdrun_461 -ntmpi 1 -gpu_id 1 -s md0-25.tpr Note: file tpx version 73, software tpx version 83 NOTE: Error occurred during GPU detection: no CUDA-capable device is detected Can not use GPU acceleration, will fall back to CPU kernels. No GPUs detected --- Program mdrun_461, VERSION 4.6.1 Source code file: /home/sudip/RPMs/gromacs-4.6.1/src/gmxlib/gmx_detect_hardware.c, line: 580 Fatal error: Some of the requested GPUs do not exist, behave strangely, or are not compatible: GPU #1: inexistent Cheers, berk Date: Thu, 28 Mar 2013 10:51:58 +0200 Subject: Re: [gmx-users] no CUDA-capable device is detected From: g...@bioacademy.gr To: gmx-users@gromacs.org Hi Chandan Are you using the same version of GCC compiler that you used to compile CUDA
Re: [gmx-users] Re: Atoms are fused after inserting in membrane
On 3/28/13 6:38 AM, Dr. Vitaly Chaban wrote: Does that mean the atoms will shrink and adjust at the time inflategro step and this closely packed lipids will stay apart? Because as you said the energy of course will be high on selected atoms during first EM step. Could you suggest me that, can I proceed as such with my system, since there is no problem in grompp and EM step (except high energy on some atom). The energy will normalize during molecular dynamics stage. ...assuming the energy is not so high as to cause an immediate crash :) -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: Atoms are fused after inserting in membrane
On 3/27/13 11:32 PM, sdshine wrote: Dear all, Does that mean the atoms will shrink and adjust at the time inflategro step and this closely packed lipids will stay apart? Because as you said the energy of course will be high on selected atoms during first EM step. Could you suggest me that, can I proceed as such with my system, since there is no problem in grompp and EM step (except high energy on some atom). or Do I need to manually remove those overlapping lipids and water molecules. No, InflateGRO does this for you. After inflation, there should be no water in the system and the lipids should have expanded outward. Any that were too close (as defined by the cutoff specified on the command line) should have been deleted. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] bond conversion between charmm and g96
On 3/28/13 5:18 AM, 라지브간디 wrote: p{margin:0;padding:0;} Dear Justin, Thank for your pointing out my issues. I just want to know how it can be converted. I have referred the equation in chapter 4 and do not know exactly how I use them. For example, The C-O bond distance and force constant written as (0.112 and 3.7000e+07 ) in gromos, whereas in charmm27 written as ( 0.1128 and 933032.0). I found the equation for g96 type covalent potential Vb (rij) and force constant Fi(rij) and don't know how do i use this for above purpose? Could you elaborate an example how it can be done? Thanks a lot. Different force fields handle bonds in different ways. Gromos96 uses a quartic bond potential (equation 4.36 in the manual), while CHARMM uses a normal harmonic potential (equation 4.34). The data in ffbonded.itp are thus interpreted differently, and in fact, when using a Gromos96 force field, the square root of bond lengths are used, etc. If you multiply the CHARMM force constant by 4, you arrive at the Gromos96 force constant (more or less). Note that force constants are irrelevant if using constraints on these bonds. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] retraining multiple protein ligand interactions using pull-code
On 3/28/13 4:01 AM, Saravanan wrote: Hello everyone, I am new to using gromacs. I am currently studying an enzyme catalysing a transfer reaction. there are two substrates and I want to restraint specific interactions between different parts of the ligands and the protein. As I understand so far from reading various discussions in the group, restraining such interactions is possible through pull code, But we can assign only one pull group0, I am wondering if there is better way to restraint multiple interactions between multiple molecules in a single simulation. If not through pull-code, what will be the best way to ensure many specific intermolecular restraints? Use distance restraints. Unfortunately, this will require a lot of topology hacking to create unified protein-ligand [moleculetype] directives. Restraints (like any bonded interaction) can only be applied within a [moleculetype], not between them. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] TOP file question
On 3/27/13 5:12 PM, Peter Eastman wrote: I'm implementing a TOP file reader, and I have a question about an ambiguity in the format. The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag can indicate that pairs are generated automatically. But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that. Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones? Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else? What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically? Which should I use? The presence of [pairs] is not dependent upon gen-pairs, but the parameters utilized by those pairs are. All force fields deal with 1-4 interactions in some way, but the manner in which they do so is different. For instance, in Gromos96 parameter sets, the gen-pairs keyword is set to no, and all pair interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, whereas for other force fields (OPLS, AMBER), the pair interactions are simply calculated according to normal combination rules with fudge factors (i.e., gen-pairs set to yes). CHARMM uses a hybrid approach wherein some pairs are set in [pairtypes], but anything not listed there is generated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] retraining multiple protein ligand interactions using pull-code
Thank you.. I hoped it would be simpler. how do I go about creating unified protein-ligand [moleculartype] directives. Can you suggest any material available on this topic? that would be extremely helpful. -Saravanan On 28 March 2013 16:45, Justin Lemkul jalem...@vt.edu wrote: On 3/28/13 4:01 AM, Saravanan wrote: Hello everyone, I am new to using gromacs. I am currently studying an enzyme catalysing a transfer reaction. there are two substrates and I want to restraint specific interactions between different parts of the ligands and the protein. As I understand so far from reading various discussions in the group, restraining such interactions is possible through pull code, But we can assign only one pull group0, I am wondering if there is better way to restraint multiple interactions between multiple molecules in a single simulation. If not through pull-code, what will be the best way to ensure many specific intermolecular restraints? Use distance restraints. Unfortunately, this will require a lot of topology hacking to create unified protein-ligand [moleculetype] directives. Restraints (like any bonded interaction) can only be applied within a [moleculetype], not between them. -Justin -- ==**== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justinhttp://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ==**== -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/**mailman/listinfo/gmx-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/**Support/Mailing_Listshttp://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] retraining multiple protein ligand interactions using pull-code
On Thu, Mar 28, 2013 at 8:18 AM, Saravanan msrvnn+...@gmail.com wrote: Thank you.. I hoped it would be simpler. how do I go about creating unified protein-ligand [moleculartype] directives. Can you suggest any material available on this topic? that would be extremely helpful. Depending on the complexity of the ligand, you may be able to do it by hand by simply adding the ligand parameters after the protein in all relevant directives of the Protein [moleculetype]. Otherwise, you will need to create an .rtp entry for the ligand and use pdb2gmx command line options to create the merged topologies (using, e.g. chain identifiers to indicate that they should be placed in the same [moleculetype] directive). In this case, refer to http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field . This is a rather advanced topic, so do as much tutorial material and other simulations as you can to familiarize yourself with a standard Gromacs workflow. You should also read Chapter 5 of the manual thoroughly to understand topology organization. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
perhaps, you could make a plot?? it is difficult to understand what you are speaking about. Dr. Vitaly Chaban On Thu, Mar 28, 2013 at 2:59 PM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] invalid pairstype 180
Dear GMX-Users I have a problem while trying to insert a drug molecule into my simulation. I have the topology file generated from the ATB-server. And accordingly I have edited the aminoacid.rtp ffbonded.itp file. I have transcribed the forcefield parameters into GROMOS96 format. here is my .itp file for that molecule. My problem is that after doing all the things when i tried to do sd minimization then i got the error message like *Program grompp, VERSION 4.5.5* *Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/kernel/topdirs.c, line: 107* * * *Fatal error:* *Invalid pairs type 180* *For more information and tips for troubleshooting, please check the GROMACS * *website at http://www.gromacs.org/Documentation/Errors* What may be the reason ? And when i studied through the .itp file then i have found the 1-4 interactions in the [ pairs ] section followed by the excluded 1-4 interactions. Now, my other question is that should I address these 1-4 interactions in the ffnonbonded.itp file ! Looking forward for kind response. [ moleculetype ] ; Name nrexcl _NW5 3 [ atoms ] ; nr type resnr resid atom cgnr chargemasstotal_charge 1 CH31_NW5C141 -0.000 15.0350 ; 0.000 2 C1_NW5 C82 -0.217 12.0110 3HC1_NW5 H120.138 1.0080 4 C1_NW5C112 -0.111 12.0110 5 C1_NW5C1520.717 12.0110 6 O1_NW5 O12 -0.580 15.9994 7 N1_NW5 N22 -0.663 14.0067 8 H1_NW5 H820.372 1.0080 9 C1_NW5C1620.785 12.0110 10NT1_NW5 N52 -0.939 14.0067 11 H1_NW5 H920.398 1.0080 12 H1_NW5H1020.398 1.0080 13NR1_NW5 N12 -0.841 14.0067 14 H1_NW5 H720.347 1.0080 15 C1_NW5 C120.040 12.0110 16 C1_NW5 C220.040 12.0110 17 C1_NW5 C32 -0.151 12.0110 18 C1_NW5 C520.150 12.0110 19 C1_NW5C1320.149 12.0110 20HC1_NW5H1420.099 1.0080 21NR1_NW5 N32 -0.567 14.0067 22NR1_NW5 N420.436 14.0067 ; 0.000 23 C1_NW5C103 -0.154 12.0110 24HC1_NW5 H630.154 1.0080 ; 0.000 25 C1_NW5 C64 -0.154 12.0110 26HC1_NW5 H340.154 1.0080 ; 0.000 27 C1_NW5 C45 -0.154 12.0110 28HC1_NW5 H250.154 1.0080 ; 0.000 29 C1_NW5 C96 -0.152 12.0110 30HC1_NW5 H560.152 1.0080 ; 0.000 31 C1_NW5 C77 -0.154 12.0110 32HC1_NW5 H470.154 1.0080 ; 0.000 33 C1_NW5C128 -0.200 12.0110 34HC1_NW5H1580.200 1.0080 ; 0.000 ; total charge of the molecule: 0.000 [ bonds ] ; ai aj funct c0 c1 1 222 0.1470 8.7100e+06 232 0.1090 1.2300e+07 242 0.1390 8.6600e+06 2 182 0.1435 6.1000e+06 452 0.1520 5.4300e+06 4 232 0.1435 6.1000e+06 562 0.1230 1.6600e+07 572 0.1380 1.1000e+07 782 0.1000 1.8700e+07 792 0.1400 8.5400e+06 9 102 0.1400 8.5400e+06 9 132 0.1320 1.2000e+07 10 112 0.1000 1.8700e+07 10 122 0.1000 1.8700e+07 13 142 0.1000 1.8700e+07 15 162 0.1435 6.1000e+06 15 172 0.1480 5.7300e+06 15 272 0.1390 8.6600e+06 16 182 0.1435 6.1000e+06 16 252 0.1435 6.1000e+06 17 192 0.1390 8.6600e+06 17 332 0.1390 8.6600e+06 18 312 0.1435 6.1000e+06 19 202 0.1090 1.2300e+07 19 212 0.1330 1.0600e+07 21 222 0.1360 4.7700e+06 22 332 0.1350 1.0300e+07 23 242 0.1090 1.2300e+07 23 252 0.1390 1.0800e+07 25 262 0.1090 1.2300e+07 27 282 0.1090 1.2300e+07 27 292 0.1435 6.1000e+06 29 302 0.1090 1.2300e+07 29 312 0.1390 1.0800e+07 31 322 0.1090 1.2300e+07 33 342 0.1090 1.2300e+07 [ pairs ] ; ai aj funct ; all 1-4 pairs but the ones excluded in GROMOS itp 261 271 481 491 5 101 5 131 681 691 6 231 7 111 7 121 7 141 7 231 8 101 8 131 10 141 11 131 12 131 16 19
Re: [gmx-users] TOP file question
Hi Justin, So if I understand you correctly, there are actually three different ways the parameters can be specified. In order of decreasing precedence: 1. If there's a [pairs] line and it includes parameters, use those parameters. 2. If there's a [pairs] line and it doesn't include parameters, look for a corresponding [pairtypes] lines and, if we find one, use that. 3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair). Is that correct? Thanks! Peter On Mar 28, 2013, at 4:20 AM, Justin Lemkul jalem...@vt.edu wrote: On 3/27/13 5:12 PM, Peter Eastman wrote: I'm implementing a TOP file reader, and I have a question about an ambiguity in the format. The [ pairs ] block lists atom pairs that should be handled specially (exclusions and 1-4 interactions). In addition, the gen-pairs flag can indicate that pairs are generated automatically. But all the files I've looked at include BOTH of these things, and I'm not sure how to interpret that. Can I assume that all pairs generated by gen-pairs are already included in the list, or might I have to generate additional ones? Can I assume that all pairs listed in the file where generated by gen-pairs, or might there be additional pairs that came from somewhere else? What if the two definitions disagree with each other, and the [ pairs ] block lists different parameters for a pair than would be generated automatically? Which should I use? The presence of [pairs] is not dependent upon gen-pairs, but the parameters utilized by those pairs are. All force fields deal with 1-4 interactions in some way, but the manner in which they do so is different. For instance, in Gromos96 parameter sets, the gen-pairs keyword is set to no, and all pair interactions are looked up from the [pairtypes] directive in ffnonbonded.itp, whereas for other force fields (OPLS, AMBER), the pair interactions are simply calculated according to normal combination rules with fudge factors (i.e., gen-pairs set to yes). CHARMM uses a hybrid approach wherein some pairs are set in [pairtypes], but anything not listed there is generated. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] Virtual sites setting
Dear gmx, I would like to set virtual sites for CO molecules with some specific charge. As per GROMACS manual, I've created virtual site2 in topology file for CO. Also, given the information in .rtp file as well as added the COM(center of mass) atom in .gro file. However, when I use gromp, it shows COM not found. Please need an advice. Thanks. Rajiv-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] Freezing group
Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use a R.E.D.III server. As there are several different fitting methods, so I have to carry out a series of short MDs (about 5-10 ns) for each of them. The question is - is it possible to isolate this domain and fix/freeze last residues of the hairpin/linker to prevent movement of domain segments? I know that this is not the way to study ligand-protein interaction, however I just want to use it for understanding which topology generation method is better. Thank you! -- * Nemo me impune lacessit* -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] no CUDA-capable device is detected
Hi, I'm glad that it got figured out. For all those who might be wondering what exactly are you referring to here is a quick summary. The NVIDIA driver needs /dev entries to be present for the GPU devices in use and these entries need the right permissions in order to allow user-space programs to access the devices (and the lack of permission was causing trouble in the above case). These entries are automatically created by the X server and the driver kernel module is also loaded when X starts. However, when using a headless (i.e server/without X) installation, what's otherwise automatically done by when X starts needs to be done manually. It is easiest to do it using an init script (or equivalent). For an example here's the init script I use on Ubuntu machines: http://pastebin.com/zs9Ve9qP. It works for me well, but use it at your own risk ;) Cheers, -- Szilárd On Thu, Mar 28, 2013 at 12:03 PM, Chandan Choudhury iitd...@gmail.comwrote: Hi !! I problem with the permission of /dev/nvidia* changed it to 0666 /dev/nvidia* Everything resolved. mdrun can be executed as normal user. Thanks everyone. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Thu, Mar 28, 2013 at 4:26 PM, Chandan Choudhury iitd...@gmail.com wrote: On Thu, Mar 28, 2013 at 4:09 PM, Szilárd Páll szilard.p...@cbr.su.se wrote: Hi, If mdrun says that it could not detect GPUs it simply means that the GPU enumeration found no GPUs, otherwise it would have printed what was found. This is rather strange because mdrun uses the same mechanism the deviceQuery SDK example. I really don't have a good idea what could be the issue, but you could try recompiling or compiling with CUDA 4.2 to see if any of that makes a difference. Let us know if you figured out something. Cheers, Thanks Szilárd for the eye opening comment. I just tried running gromacs as root. I recalled I had executed deviceQuery as root. While executing as user it produces the same error : */root/NVIDIA_CUDA-5.0_Samples/1_Utilities/deviceQuery/deviceQuery Starting... CUDA Device Query (Runtime API) version (CUDART static linking) cudaGetDeviceCount returned 38 - no CUDA-capable device is detected* Now, running gromacs as root, it is running successfully (I suppose). Output of nvidia-smi +--+ | NVIDIA-SMI 4.310.40 Driver Version: 310.40 | |---+--+--+ | GPU Name | Bus-IdDisp. | Volatile Uncorr. ECC | | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. | |===+==+==| | 0 NVS 300 | :03:00.0 N/A | N/A | | N/A 48C N/A N/A / N/A | 3% 17MB / 511MB | N/A Default | +---+--+--+ | 1 Tesla K20c | :04:00.0 Off | Off | | 50% 62CP0 106W / 225W | 2% 87MB / 5119MB | 76% Default | +---+--+--+ +-+ | Compute processes: GPU Memory | | GPU PID Process name Usage | |=| |0Not Supported | |1 9127 mdrun_461 72MB | +-+ Output of md.log 2 GPUs detected: #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: no, stat: compatible #1: NVIDIA NVS 300, compute cap.: 1.2, ECC: no, stat: incompatible 1 GPU auto-selected for this run: #0 I think there is something relate to permissions. Though nvcc has 755 permission, something else might require additional permissions. Chandan -- Szilárd On Thu, Mar 28, 2013 at 2:39 AM, Berk Hess g...@hotmail.com wrote: Hi, I am not the expert on GPU detection, so we'll need to wait until an expert replies. Maybe GPU 0 is ignored and the GPUs are renumbered, could you try: mdrun -ntmpi 1 -gpu_id 0 Also your tpr file is from an older version. It will not run on a GPU. You need to set the mdp option: cutoff-scheme = Verlet and run grompp to get a new tpr file. Cheers, Berk From: iitd...@gmail.com Date: Thu, 28 Mar 2013 14:57:16 +0530 Subject: Re: [gmx-users] no CUDA-capable device is detected To: gmx-users@gromacs.org On Thu, Mar 28, 2013 at 2:41 PM, Berk Hess g...@hotmail.com wrote: Hi, The code compiled, so the compiler is not the issue.
Re: [gmx-users] TOP file question
3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair). Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a [pairs] record for each 1-4. Peter-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
The simplest advice is to increase sampling. Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] TOP file question
After further study of the documentation, I find myself getting more confused rather than less. I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not Coulomb parameters. (There's a function type 2 for [pairs] that does include charges, but the manual says that function type is only used for free energy calculations.) How do I select the latter when gen-pairs is off? Is it simply assumed that 1-4 Coulomb interactions are never reduced for force fields that don't use gen-pairs? Table 5.5 lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as LJ. But no other mention of this directive appears anywhere else in the manual, there doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that pairs_nb never occurs in any file in the entire top directory. What am I misunderstanding? Peter-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] Virtual sites setting
Dear Rajiv, Without a clear explanation of what you are doing and the specific error message from grompp it is impossible to offer any sensible advice. Other pieces of information which might be useful would be, the topology file, the actual grompp line, and the gro file for a single CO molecule Richard On 28/03/2013 20:02, 라지브간디 ra...@kaist.ac.kr wrote: Dear gmx, I would like to set virtual sites for CO molecules with some specific charge. As per GROMACS manual, I've created virtual site2 in topology file for CO. Also, given the information in .rtp file as well as added the COM(center of mass) atom in .gro file. However, when I use gromp, it shows COM not found. Please need an advice. Thanks. Rajiv -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] TOP file question
On 3/28/13 7:14 PM, Peter Eastman wrote: 3. If gen-pairs is yes, then generate parameters for all 1-2, 1-3, and 1-4 pairs for which we did not already find parameters in step 1 or 2 (regardless of whether or not a [pairs] line exists for a particular pair). Or rather, generate an [exclusions] record for each 1-2 and 1-3, and a [pairs] record for each 1-4. Not quite. The presence of an entry in [pairs] is required. When processing the topology, grompp doesn't do any magic. It won't generate pair interactions for any combination for which there is no entry. I think gen-pairs is somewhat misleading. It doesn't generate pairs. It generates parameters for the pairs that the user (or pdb2gmx/g_x2top) has listed, which assumes proper use of the force field. For a bit more discussion of how this all works: http://lists.gromacs.org/pipermail/gmx-users/2012-December/077005.html -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] TOP file question
On 3/28/13 8:25 PM, Peter Eastman wrote: After further study of the documentation, I find myself getting more confused rather than less. I see that the [pairs] and [pairtypes] directives only specify LJ parameters, not Coulomb parameters. (There's a function type 2 for [pairs] that does include charges, but the manual says that function type is only used for free energy calculations.) How do I select the latter when gen-pairs is off? Is it simply assumed that 1-4 Coulomb interactions are never reduced for force fields that don't use gen-pairs? Table 5.5 lists an alternate directive, [pairs_nb] that does specify Coulomb parameters as well as LJ. But no other mention of this directive appears anywhere else in the manual, there doesn't seem to be any corresponding [pairtypes] option, and a grep reveals that pairs_nb never occurs in any file in the entire top directory. What am I misunderstanding? Which version of the manual are you using? I recall the discussion on [pairs_nb] being absent in an older version, but manual section 5.3.4 in version 4.6.1 has lots of discussion on [pairs_nb]. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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: diffusion constant level off
On 3/28/13 5:32 PM, Ahmet yıldırım wrote: Please see plot: http://imageshack.us/photo/my-images/35/diffusion.png/ How did you come up with your expected values? What does the original msd.xvg plot look like? It should be basically linear. If it's not, then you have found the source of your problem. -Justin 2013/3/28 Justin Lemkul jalem...@vt.edu On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım ahmedo...@gmail.com wrote: Dear users, Again, I have strange results (for 10,50,100,150,200 ns). I am wondering, is there a bug with g_msd? I see no evidence for a bug, and you should avoid such speculation unless you know exactly how the program should behave. Only then, after an analysis of known quantities or behavior, can we discuss bugginess. Do you know how g_msd works? Do you know what all of the flags are doing, or are you just making adjustments hoping for clarity? You may find the following post very illuminating: http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html -Justin Commands for trestart to 20 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 19 -e 20 Commands for trestart to 1000 ps: g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 1 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 2 -e 3 ... g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1 -endfit -1 -b 19 -e 20 D1 (cm^2/s):Diffusion for trestart to 20 ps D2 (cm^2/s):Diffusion for trestart to 1000 ps Time (ns) D1 D2 10 0.1616 0.1091 20 0.0735 0.0679 30 0.0775 0.0705 40 0.1097 0.1189 50 0.1471 0.1436 60 0.0468 0.048 70 0.0667 0.0652 80 0.0727 0.086 90 0.0664 0.0707 100 0.1336 0.114 110 0.0899 0.0841 120 0.0572 0.0598 130 0.0506 0.0482 140 0.0723 0.0767 150 0.1466 0.1439 160 0.0703 0.0601 170 0.081 0.0853 180 0.0278 0.027 190 0.1121 0.1024 200 0.3136 0.2981 2013/3/28 Dr. Vitaly Chaban vvcha...@gmail.com if I do as you said, I will get only one diffusion coefficient. I want to calculate one diffusion coefficient for each 10 ns of the simulation time of 200 ns. That is, I want to get 20 diffusion values. 2013/3/28 David van der Spoel sp...@xray.bmc.uu.se On 2013-03-28 10:40, Ahmet yıldırım wrote: Dear users, This time, I calculated the diffusion coefficients of protein for each 10 ns of the simulation providing a total simulation time of 200 ns. g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1 -endfit -1 -b 0 -e 1 g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1 -endfit -1 -b 10001 -e 2 g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1 -endfit -1 -b 20001 -e 3 g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1 -endfit -1 -b 190001 -e 20 Set trestart to 10001 (no restarts), or do one run with g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1 I believe the advice was to increase trestart and you can decide yourself how much to increase. Most likely, your protein deserves better sampling than 10 ns for a linear diffusion. Dr. Vitaly Chaban -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Ahmet Yıldırım -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to
Re: [gmx-users] RE: diffusion constant level off
On 3/28/13 7:56 PM, Dr. Vitaly Chaban wrote: The simplest advice is to increase sampling. I think the OP needs to describe what the system is in greater detail. For a simple liquid, I would opine that 200 ns is normally vast overkill. For a membrane, it may not be enough. There's just no way to say. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] chiller failure leads to truncated .cpt and _prev.cpt files using gromacs 4.6.1
Thank you, Berk, Justin, and Matthew, for your assistance. I checked with my sysadmin, who said: The /global/scratch FS is Lustre. It is fully POSIX and the fsync etc are fully and well implemented. However when the 'power off' command is issued there is no way OS can finish I/O in a controlled way. Note that the power off command was given when they realized that they had lost all cooling in the data room, and they had just a few minutes to react, forcing them to shutdown all compute nodes. Justin's suggestion to use -cpnum is good, although I think it will be easier to simply have a script that runs gmxcheck once every 12 hours and backs up the .cpt file if it is ok. I don't know enough about computer OS's to say if there is any possible way for gromacs to avoid this in the future, but if it was possible, then it would be useful. Thank you again, Chris. -- original message -- Gromacs calls fsync for every checkpoint file written: fsync() transfers (flushes) all modified in-core data of (i.e., modi- fied buffer cache pages for) the file referred to by the file descrip- tor fd to the disk device (or other permanent storage device) so that all changed information can be retrieved even after the system crashed or was rebooted. This includes writing through or flushing a disk cache if present. The call blocks until the device reports that the transfer has completed. It also flushes metadata information associ- ated with the file (see stat(2)). If fsync fails, mdrun exits with a fatal error. We have experience with unreliable AFS file systems, where fsync mdrun could wait for hours and fail, for which we added an environment variable. So either fsync is not supported on your system (highly unlikely) or your file system returns 0, indicating the file was synched, but it actually didn't fully sync. Note that we first write a new checkpoint file with number, fynsc that, then move the current to _prev (thereby loosing the old prev) and then the numbered one to the current. So you should never end up with only corrupted files, unless fsync doesn't do what it's supposed to do. Cheers, Berk -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] Freezing group
On 3/28/13 4:24 PM, Алексей Раевский wrote: Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use a R.E.D.III server. As there are several different fitting methods, so I have to carry out a series of short MDs (about 5-10 ns) for each of them. The question is - is it possible to isolate this domain and fix/freeze last residues of the hairpin/linker to prevent movement of domain segments? I know that this is not the way to study ligand-protein interaction, however I just want to use it for understanding which topology generation method is better. You can freeze whatever group you want using freezegrps and a custom index group. It is also reasonably simple to restrain a segment of the structure using normal position restraints (again, created with a custom index group). -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists