Re: [gmx-users] quick question about restart
On 29/02/2012 9:47 PM, Anna Marabotti wrote: Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I have two possibilities: First approach: I'm setting within the .mdp file a global duration of 100 ns. Then: grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, I see that the run has been stopped after 10 ns. I have the output_fullMD.cpt file. Then, I do: mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the run has been completed (then I will concatenate the .xtc, .edr, .trr files) Yep, or use the same -deffnm filename and -append for more simplicity. See http://www.gromacs.org/Documentation/How-tos/Doing_Restarts#section_2 Second approach: I'm setting within the .mdp file a global duration of 10 ns. Then (as above): grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, the run has been finished. Then, I continue the run for other 10 ns with: tpbconv -s input_fullMD.tpr -extend 1 -o input_fullMD_2.tpr mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the 100-ns run has been completed. Are the two procedure producing EXACTLY the same results, or not? In principle, they are implementing the same algorithm over the 10 runs. In practice, the discussion at http://www.gromacs.org/Documentation/Terminology/Reproducibility applies and you will likely not observe an identical trajectory from each case. In theory, mdrun -reprod does a better job in many cases for often losing performance, but random number states are not preserved, so various algorithms cannot be reproducible across restarts. Which is the best preferred procedure? The first, with appending, is simple and requires no concatenation post-processing. Feel free to back up your files between runs if you want insurance against loss - but you should do that anyway. Anything else requires you to do more work later on for no gain. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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] quick question about restart
I use the second option there on all my simulations, using a script. Simulations are done in 10ns blocks, at the completion of that the pbs script submits the next job. Have found this way much less hassle, better computer utilisation etc. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9903 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Anna Marabotti Sent: Wednesday, 29 February 2012 9:48 PM To: gmx-users@gromacs.org Subject: [gmx-users] quick question about restart Dear gmx-users, I'm running my simulations on a machine with a queue system that stops the runs longer than 24 hours. Often, for my simulations, I need a longer time to complete the runs. Let's have an example. I have to run a 100ns-long simulation on a machine that produces 10ns/days simulation. I have two possibilities: First approach: I'm setting within the .mdp file a global duration of 100 ns. Then: grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, I see that the run has been stopped after 10 ns. I have the output_fullMD.cpt file. Then, I do: mdrun -s input_fullMD.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the run has been completed (then I will concatenate the .xtc, .edr, .trr files) Second approach: I'm setting within the .mdp file a global duration of 10 ns. Then (as above): grompp -f param.mdp -c prot.gro -p topol.top -o input_fullMD.tpr mdrun -s input_fullMD.tpr -deffnm output_fullMD After 24 h, the run has been finished. Then, I continue the run for other 10 ns with: tpbconv -s input_fullMD.tpr -extend 1 -o input_fullMD_2.tpr mdrun -s input_fullMD_2.tpr -cpi output_fullMD.cpt -deffnm output_fullMD_2 and so on for 10 days, until the 100-ns run has been completed. Are the two procedure producing EXACTLY the same results, or not? Which is the best preferred procedure? Thank you very much Anna Anna Marabotti, Ph.D. Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm When a man with a gun meets a man with a pen, the man with a gun is a dead man (Roberto Benigni, about Roberto Saviano) -- 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
