Re: [gmx-users] Extending simulation problem.
2014-08-21 17:45 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Well in my *log file nothing about state or *cpi files is mentioned. Sounds like perhaps your combination of circumstances (-append, no old output files provided for appending, maybe not even a checkpoint file provided) is leading to mdrun silently doing the only thing it can do, which is start again from either the -s or -cpi state. Your description of I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same doesn't help fully - same as what? The start of the first simulation, or the end of the first simulation? It is exactly the same as the start of the first simulation. Like I said, I did not have appropriate files from previous simulation in my scratch and I rerun it incorrectly I guess. Thank you for your detailed answer :). I think I will manage now to extend this simulation properly. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending simulation problem.
Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length 5000 steps... time 0.000 and length 10.000 ps So it looks like new status file is written and it says that simulation will start from the very beginning or did I misunderstand something? However when I check state.cpt with gmxdump it looks fine: step = 250 t = 5000.00 as I expect. Thank you, Dawid 2014-08-22 13:15 GMT+01:00 Dawid das add...@googlemail.com: 2014-08-21 17:45 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Well in my *log file nothing about state or *cpi files is mentioned. Sounds like perhaps your combination of circumstances (-append, no old output files provided for appending, maybe not even a checkpoint file provided) is leading to mdrun silently doing the only thing it can do, which is start again from either the -s or -cpi state. Your description of I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same doesn't help fully - same as what? The start of the first simulation, or the end of the first simulation? It is exactly the same as the start of the first simulation. Like I said, I did not have appropriate files from previous simulation in my scratch and I rerun it incorrectly I guess. Thank you for your detailed answer :). I think I will manage now to extend this simulation properly. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending simulation problem.
On 8/22/14, 8:49 AM, Dawid das wrote: Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length 5000 steps... time 0.000 and length 10.000 ps So it looks like new status file is written and it says that simulation will start from the very beginning or did I misunderstand something? However when I check state.cpt with gmxdump it looks fine: step = 250 t = 5000.00 All of this is expected. Using tpbconv doesn't change the start time of the .tpr file. It says the new .tpr file has a new number of steps and the starting step is determined by the use of a checkpoint file on the mdrun command line. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending simulation problem.
On Aug 22, 2014 2:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/22/14, 8:49 AM, Dawid das wrote: Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length 5000 steps... time 0.000 and length 10.000 ps So it looks like new status file is written and it says that simulation will start from the very beginning or did I misunderstand something? However when I check state.cpt with gmxdump it looks fine: step = 250 t = 5000.00 All of this is expected. Using tpbconv doesn't change the start time of the .tpr file. It says the new .tpr file has a new number of steps and the starting step is determined by the use of a checkpoint file on the mdrun command line. ... And falling back on the contents of the .tpr to start at the designated start time, if there's no checkpoint provided. Mark -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending simulation problem.
Well in my *log file nothing about state or *cpi files is mentioned. Acutally I have a question regarding state.cpi files. Does it contain names of *gro, *trr, etc. files if they are not standard? The thing is, that output files from my first 5ns simulation are not standard. Now, I perform these calculations not in my working directory but on separate scratch. In this case, should the output files from previous simulation be present in the scratch? And when I run another 5 ns should I run mdrun with those -c -o and -e options? If yes, should the names of files be the same as in the previous simulation? 2014-08-20 18:18 GMT+01:00 Justin Lemkul jalem...@vt.edu: On 8/20/14, 6:33 AM, Dawid das wrote: Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_ protein_simulation_in_Gromacs_from_1000_ps_to_1_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr $CURDIR/mCherry7-npt-md.log 21 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong? What does the .log file say? It should clearly indicate if the restart was done by reading in the checkpoint file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Extending simulation problem.
Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr $CURDIR/mCherry7-npt-md.log 21 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong? Best wishes, Dawid Grabarek -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending simulation problem.
Oh I forgot that I used -append option in the latter \$MDRUN command: \$MDRUN -s npt-md-ext.tpr -cpi state.cpt -append 2014-08-20 11:33 GMT+01:00 Dawid das add...@googlemail.com: Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr $CURDIR/mCherry7-npt-md.log 21 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong? Best wishes, Dawid Grabarek -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Extending simulation problem.
On 8/20/14, 6:33 AM, Dawid das wrote: Dear Gromacs experts, I googled for answer and I found these: http://www.gromacs.org/Documentation/How-tos/Extending_Simulations http://www.researchgate.net/post/How_to_extend_the_protein_simulation_in_Gromacs_from_1000_ps_to_1_ps but still I am confused about what happens in my simulation. I did 5 ns simulation and I would like to add extra 5 ns on top of that so that new results (energies, temperature, trajectory, etc.) will be appended to already existing files after first 5 ns simulation. Now I used this command to run MD simulation for the first time: \$MDRUN -v -s npt-md.tpr -o mCherry7-npt-md.trr -c mCherry7-npt-md.gro -e mCherry7-npt-md.edr $CURDIR/mCherry7-npt-md.log 21 After this in the same directory I run: tpbconv -s npt-md.tpr -extend 5000 -o npt-md-ext.tpr \$MDRUN -s npt-md-ext.tpr -cpi state.cpt I tried both state.cpt and prev_state.cpt and the beginning of new simulation looks exactly the same that means temperature, energies, etc. are the same as if I started from 0ns step, not from 5ns step of previous simulation. What can cause that? Is it because of used files names or I did something else wrong? What does the .log file say? It should clearly indicate if the restart was done by reading in the checkpoint file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
