[gmx-users] about command do_dssp
Dear prof. i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use the do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg to analyze the secondary structrue of the protein. when i perform the do_dssp and select MainChain , the fatal erros come out as follow; Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) it is means thant i don't install do_dssp? however, when i perform the which do_dssp at the terminal, the termianl output /usr/local/gromacs-4.6.1/bin/do_dssp. i don't know where is wrong. should i reset the environment of the do_dssp? please help me ! -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] Including polarizability by a Drude oscillator or the shell model
On 2013-04-27 19:18, Andrew DeYoung wrote: Hi, I am interested in including polarizability using a Drude harmonic oscillator (charge on a spring). In section 3.5 of the version 4.5.4 manual, Shell molecular dynamics is described briefly. It seems that the shell model is quite similar, if not identical, to the Drude oscillator. However, I do not see in the manual where the use of the shell model in Gromacs simulations is described. Do you know if some sort of tutorial exists about the use of the shell model (or the Drude oscillator) in Gromacs? Thank you so much for your time! Andrew DeYoung Carnegie Mellon University Check here for some examples http://virtualchemistry.org/pol.php -- 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] can we use large timestep for membrane GPU simulation?
Hello: I am watching Eric online Gromacs GPU webminar these days. I notice that he talked about introduce large timestep (5fs) for GPU simulations on a water system. I am just wondering, can we also introduce such big time step for membrane system if we are going to run the job in Gromacs? What's more, Eric also shown the GLIC ion channel simulation with 150,000 atoms. E5-2690+GTX Titan can get up to 38ns/day. But he didn't talked about what's the timestep and cutoff. could anybody comment on this? thank you very much best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] about command do_dssp
On 4/28/13 4:07 AM, aixintiankong wrote: Dear prof. i use the the gromacs 4.6.1 on my centos6.4 system. After MD ending, i use the do_dssp -f md.xtc -s md.tpr -o secondary-structure.xpm -sc secondary-structure.xvg to analyze the secondary structrue of the protein. when i perform the do_dssp and select MainChain , the fatal erros come out as follow; Fatal error: DSSP executable (usr/local/bin/dssp) does not exist (use setenv DSSP) it is means thant i don't install do_dssp? however, when i perform the which do_dssp at the terminal, the termianl output /usr/local/gromacs-4.6.1/bin/do_dssp. i don't know where is wrong. should i reset the environment of the do_dssp? do_dssp and dssp are different executables. Please read the following: http://www.gromacs.org/Documentation/Gromacs_Utilities/do_dssp -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] why files are so large?
Hello: I am using the following settings for output file: dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout = 500 ; Write coordinates to output .trr file every 2 ps nstvout = 500 ; Write velocities to output .trr file every 2 ps nstfout = 0 nstxtcout = 5 nstenergy = 50; Write energies to output .edr file every 2 ps nstlog = 50; Write output to .log file every 2 ps and I obtained following warnings from grompp: NOTE 2 [file md.mdp]: This run will generate roughly 2791985478365075968 Mb of data however, when I set nstxout=0 nstvout=0 nstoout=0 I obtained following informations: This run will generate roughly -9066 Mb of data why it file size is negative? Moreover, my nstxout is very large, I don't know why the file is so big and no matter how did I change nstxout, nstvout, the files size doesn't change at all. it always claimed: This run will generate roughly 2791985478365075968 Mb of data thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] can we use large timestep for membrane GPU simulation?
On 4/28/13 6:15 AM, Albert wrote: Hello: I am watching Eric online Gromacs GPU webminar these days. I notice that he talked about introduce large timestep (5fs) for GPU simulations on a water system. I am just wondering, can we also introduce such big time step for membrane system if we are going to run the job in Gromacs? The key to using a 5-fs timestep is constraining all bonds and using virtual sites. If you do this, you can use such a timestep with just about any system. What's more, Eric also shown the GLIC ion channel simulation with 150,000 atoms. E5-2690+GTX Titan can get up to 38ns/day. But he didn't talked about what's the timestep and cutoff. Can't comment on this part. -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] why files are so large?
On 4/28/13 8:04 AM, Albert wrote: Hello: I am using the following settings for output file: dt = 0.002 ; Time-step (ps) nsteps = 25; Number of steps to run (0.002 * 50 = 1 ns) ; Parameters controlling output writing nstxout = 500 ; Write coordinates to output .trr file every 2 ps nstvout = 500 ; Write velocities to output .trr file every 2 ps nstfout = 0 nstxtcout = 5 nstenergy = 50; Write energies to output .edr file every 2 ps nstlog = 50; Write output to .log file every 2 ps and I obtained following warnings from grompp: NOTE 2 [file md.mdp]: This run will generate roughly 2791985478365075968 Mb of data however, when I set nstxout=0 nstvout=0 nstoout=0 I obtained following informations: This run will generate roughly -9066 Mb of data why it file size is negative? Moreover, my nstxout is very large, I don't know why the file is so big and no matter how did I change nstxout, nstvout, the files size doesn't change at all. it always claimed: This run will generate roughly 2791985478365075968 Mb of data This looks like a pretty clear bug to me, especially the negative file size, which cannot possibly make sense. What version of Gromacs is this? -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] why files are so large?
On 04/28/2013 02:08 PM, Justin Lemkul wrote: This looks like a pretty clear bug to me, especially the negative file size, which cannot possibly make sense. What version of Gromacs is this? -Justin hi Justin: thanks a lot for kind comments. I am using the latest 4.6.1 with GPU production. best Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] why files are so large?
On 4/28/13 8:09 AM, Albert wrote: On 04/28/2013 02:08 PM, Justin Lemkul wrote: This looks like a pretty clear bug to me, especially the negative file size, which cannot possibly make sense. What version of Gromacs is this? -Justin hi Justin: thanks a lot for kind comments. I am using the latest 4.6.1 with GPU production. Please file a bug report on redmine.gromacs.org, including the exact screen output and all files necessary to reproduce the problem. -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] GPU job often stopped
Dear: I am running MD jobs in a workstation with 4 K20 GPU and I found that the job always failed with following messages from time to time: [tesla:03432] *** Process received signal *** [tesla:03432] Signal: Segmentation fault (11) [tesla:03432] Signal code: Address not mapped (1) [tesla:03432] Failing at address: 0xfffe02de67e0 [tesla:03432] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7f4666da1cb0] [tesla:03432] [ 1] mdrun_mpi() [0x47dd61] [tesla:03432] [ 2] mdrun_mpi() [0x47d8ae] [tesla:03432] [ 3] /opt/intel/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x7f46667904f3] [tesla:03432] *** End of error message *** -- mpirun noticed that process rank 0 with PID 3432 on node tesla exited on signal 11 (Segmentation fault). -- I can continue the jobs with mdrun option -append -cpi, but it still stopped from time to time. I am just wondering what's the problem? thank you very much Albert -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. 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] GPU job often stopped
On 4/28/13 11:27 AM, Albert wrote: Dear: I am running MD jobs in a workstation with 4 K20 GPU and I found that the job always failed with following messages from time to time: [tesla:03432] *** Process received signal *** [tesla:03432] Signal: Segmentation fault (11) [tesla:03432] Signal code: Address not mapped (1) [tesla:03432] Failing at address: 0xfffe02de67e0 [tesla:03432] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0xfcb0) [0x7f4666da1cb0] [tesla:03432] [ 1] mdrun_mpi() [0x47dd61] [tesla:03432] [ 2] mdrun_mpi() [0x47d8ae] [tesla:03432] [ 3] /opt/intel/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93) [0x7f46667904f3] [tesla:03432] *** End of error message *** -- mpirun noticed that process rank 0 with PID 3432 on node tesla exited on signal 11 (Segmentation fault). -- I can continue the jobs with mdrun option -append -cpi, but it still stopped from time to time. I am just wondering what's the problem? Frequent failures suggest instability in the simulated system. Check your .log file or stderr for informative Gromacs diagnostic information. -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
