[gmx-users] About extend the run,,
Hi Gromacs Friends, I run a Production run with saving the co-ordinates and velocity after every 500 steps for 20ns.. Now I want to extend the run but with saving the co-ordinates and velocity after every 1000 steps for next 30ns (total 50ns) To perform these task I am using following command 1. grompp -f New mdp file just change in saving output -t .cpt -c .gro file(gro file from position restrained run ) -o new.tpr 2. tpbconv -s new.tpr -0 extend.tpr -extend 3 3. mdrun -v -deffnm extend -cpi .cpt -append Is these approach is correct?? Second query; To rerun the crash run, users give .cpt file as input to -mdrun, My query is, There are two cpt file a) pre.cpt b) .cpt , So which one has to given as input??? All suggestion are welcome... With Best Wishes, Rama david -- 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 extend the run,,
On 6/2/12 10:27 AM, rama david wrote: Hi Gromacs Friends, I run a Production run with saving the co-ordinates and velocity after every 500 steps for 20ns.. Now I want to extend the run but with saving the co-ordinates and velocity after every 1000 steps for next 30ns (total 50ns) To perform these task I am using following command 1. grompp -f New mdp file just change in saving output -t .cpt -c .gro file(gro file from position restrained run ) -o new.tpr 2. tpbconv -s new.tpr -0 extend.tpr -extend 3 3. mdrun -v -deffnm extend -cpi .cpt -append Is these approach is correct?? No. The new.tpr file contains instructions to run from 20 - 30 ns. There is no need to then invoke tpbconv. You would also need a new invocation of mdrun, since the output frequencies won't match. You don't want to append those files with mdrun (nor will the checkpoint file likely let you). Second query; To rerun the crash run, users give .cpt file as input to -mdrun, My query is, There are two cpt file a) pre.cpt b) .cpt , So which one has to given as input??? Use gmxcheck to understand the contents of each. The timestamp will also tell you a difference, as will reading mdrun -h for an explanation of what the -cpt option is doing. -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] About extend the run,,
Thank you Justin for quick reply On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu wrote: To perform these task I am using following command 1. grompp -f New mdp file just change in saving output -t .cpt -c .gro file(gro file from position restrained run ) -o new.tpr 2. tpbconv -s new.tpr -0 extend.tpr -extend 3 3. mdrun -v -deffnm extend -cpi .cpt -append Is these approach is correct?? No. The new.tpr file contains instructions to run from 20 - 30 ns. There is no need to then invoke tpbconv. You would also need a new invocation of mdrun, since the output frequencies won't match. You don't want to append those files with mdrun (nor will the checkpoint file likely let you) Extremely Sorry for my carelessness , New mdp files means the same as previous, with same number of steps, but just change in output frequency So as per your recommendation and experience Is any alternative to do these from 20 ns??? Second query; To rerun the crash run, users give .cpt file as input to -mdrun, My query is, There are two cpt file a) pre.cpt b) .cpt , So which one has to given as input??? Use gmxcheck to understand the contents of each. The timestamp will also tell you a difference, as will reading mdrun -h for an explanation of what the -cpt option is doing As per the link.. http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File I interpreted following things.. 1. I have to use the state.cpt , but in the case problem to these I have to use prev.cpt, I can check there content by gmxcheck.. But my Query is What are may be the potential problems ?? and how to find them ?? Crash the run is very often with my system, that why I am worried.. -- 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 extend the run,,
On 6/2/12 11:23 AM, rama david wrote: Thank you Justin for quick reply On Sat, Jun 2, 2012 at 8:12 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: To perform these task I am using following command 1. grompp -f New mdp file just change in saving output -t .cpt -c .gro file(gro file from position restrained run ) -o new.tpr 2. tpbconv -s new.tpr -0 extend.tpr -extend 3 3. mdrun -v -deffnm extend -cpi .cpt -append Is these approach is correct?? No. The new.tpr file contains instructions to run from 20 - 30 ns. There is no need to then invoke tpbconv. You would also need a new invocation of mdrun, since the output frequencies won't match. You don't want to append those files with mdrun (nor will the checkpoint file likely let you) Extremely Sorry for my carelessness , New mdp files means the same as previous, with same number of steps, but just change in output frequency So as per your recommendation and experience Is any alternative to do these from 20 ns??? You'll get a mismatch in your files (checkpoint, trajectory, energy) in terms of frame interval. You should not try to append to these files or extend the run. Just run a new simulation from 20 - 30 ns. The grompp command was correct, assuming you set tinit = 2 in the .mdp file and setting nsteps appropriately to give another 10 ns. Then run it as a new simulation. It will still be an extension of the first simulation (since the .cpt preserves the previous state), but without the mdrun -cpi -append mechanism, which in this case you don't want (or possibly can't use). Second query; To rerun the crash run, users give .cpt file as input to -mdrun, My query is, There are two cpt file a) pre.cpt b) .cpt , So which one has to given as input??? Use gmxcheck to understand the contents of each. The timestamp will also tell you a difference, as will reading mdrun -h for an explanation of what the -cpt option is doing As per the link..http://www.gromacs.org/Documentation/File_Formats/Checkpoint_File I interpreted following things.. 1. I have to use the state.cpt , but in the case problem to these I have to use prev.cpt, I can check there content by gmxcheck.. But my Query is What are may be the potential problems ?? and how to find them ?? Crash the run is very often with my system, that why I am worried.. If you're getting frequent crashes, you should investigate why this is happening rather than just plowing ahead. Are there error messages in the .log or stdout/stderr output? Are your energetic terms sensible? If the system is crashing due to physical instability, you're wasting your time producing junk. If the crashes are occurring due to hardware or filesystem instability, that's something to take up with your sysadmin. -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] About extend the run,,
Thank You for Quick reply Justin... On Sat, Jun 2, 2012 at 8:58 PM, Justin A. Lemkul jalem...@vt.edu wrote: You'll get a mismatch in your files (checkpoint, trajectory, energy) in terms of frame interval. You should not try to append to these files or extend the run. Just run a new simulation from 20 - 30 ns. The grompp command was correct, assuming you set tinit = 2 in the .mdp file and setting nsteps appropriately to give another 10 ns. Then run it as a new simulation. It will still be an extension of the first simulation (since the .cpt preserves the previous state), but without the mdrun -cpi -append mechanism, which in this case you don't want (or possibly can't use) I will follow your advice.. Second query; To rerun the crash run, users give .cpt file as input to -mdrun, My query is, There are two cpt file a) pre.cpt b) .cpt , So which one has to given as input??? Use gmxcheck to understand the contents of each. The timestamp will also tell you a difference, as will reading mdrun -h for an explanation of what the -cpt option is doing As per the link..http://www.gromacs.org/**Documentation/File_Formats/** Checkpoint_Filehttp://www.gromacs.org/Documentation/File_Formats/Checkpoint_File I interpreted following things.. 1. I have to use the state.cpt , but in the case problem to these I have to use prev.cpt, I can check there content by gmxcheck.. But my Query is What are may be the potential problems ?? and how to find them ?? Crash the run is very often with my system, that why I am worried.. If you're getting frequent crashes, you should investigate why this is happening rather than just plowing ahead. Are there error messages in the .log or stdout/stderr output? Are your energetic terms sensible? If the system is crashing due to physical instability, you're wasting your time producing junk. If the crashes are occurring due to hardware or filesystem instability, that's something to take up with your sysadmin. -Justin Thank you For Advice... -- 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
