Re: [gmx-users] Time frames missing
Dear Sir Is there a way to start from 159 ns and end it at 166 without checkpoint file. Because no checkpoint is there, neither it is backed up. The log file is updated till 161ns and when i give state.cpt, the fatal error occurs with the follwing msg: Cannot find log file of 145900 kb. The information in .trr says that frames till 159 ns are present but the .log file is updated till 161.. And that is also incomplete. Is there a ways to continue from 159 ..otherwise i will start from 100 ns again. Original message From: Justin Lemkul <jalem...@vt.edu> Date:02/08/2016 3:12 AM (GMT+05:30) To: gmx-us...@gromacs.org Cc: Subject: Re: [gmx-users] Time frames missing On 8/1/16 2:41 AM, Sun Iba wrote: > Hello everyone > > I have extended a 100 ns simulation of a protein in water up to 200 ns. > However, the system kept shutting down during the course of simulation and > i had to restart the runs twice. Following are the files I obtained after > completion of mdrun (I am writing information of .xtc only, for .trr its > same: > > > *md_0_1.xtc = 0 to 100 ns* > > *new.xtc = 99.990 to 159.990* > > *v.xtc = 166.050 to 179.050* > *traj-comp.xtc = 179.620 to 200.00 ns* > > Now I am surprised to see that the time frames from 159.990 to 166.050 are > not written to any file. I have also checked the .trr and .xtc file with > gmx check and found that time frames are incomplete after the follwoing > command: > > gmx check -f new.trr > > Checking file new.trr > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > # Atoms 133688 > Reading frame6000 time 159990.000 > > *WARNING: Incomplete frame: nr 6607 time 166060* > > Item#frames Timestep (ps) > Step 660710 > Time 660710 > Lambda660710 > Coords660710 > Velocities660710 > Forces 0 > Box 660710 > > Now I am not sure to catenate the avaialble file or should i start the run > again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT... > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Time frames missing
Thank you Sir but this is the first thing I looked at. Actually the checkpoint file is also missing. Sent from Samsung Mobile Original message From: Justin Lemkul <jalem...@vt.edu> Date:02/08/2016 3:12 AM (GMT+05:30) To: gmx-us...@gromacs.org Cc: Subject: Re: [gmx-users] Time frames missing On 8/1/16 2:41 AM, Sun Iba wrote: > Hello everyone > > I have extended a 100 ns simulation of a protein in water up to 200 ns. > However, the system kept shutting down during the course of simulation and > i had to restart the runs twice. Following are the files I obtained after > completion of mdrun (I am writing information of .xtc only, for .trr its > same: > > > *md_0_1.xtc = 0 to 100 ns* > > *new.xtc = 99.990 to 159.990* > > *v.xtc = 166.050 to 179.050* > *traj-comp.xtc = 179.620 to 200.00 ns* > > Now I am surprised to see that the time frames from 159.990 to 166.050 are > not written to any file. I have also checked the .trr and .xtc file with > gmx check and found that time frames are incomplete after the follwoing > command: > > gmx check -f new.trr > > Checking file new.trr > trn version: GMX_trn_file (single precision) > Reading frame 0 time 0.000 > # Atoms 133688 > Reading frame6000 time 159990.000 > > *WARNING: Incomplete frame: nr 6607 time 166060* > > Item#frames Timestep (ps) > Step 660710 > Time 660710 > Lambda660710 > Coords660710 > Velocities660710 > Forces 0 > Box 660710 > > Now I am not sure to catenate the avaialble file or should i start the run > again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT... > http://www.gromacs.org/Documentation/How-tos/Doing_Restarts -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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] Time frames missing
Hello everyone I have extended a 100 ns simulation of a protein in water up to 200 ns. However, the system kept shutting down during the course of simulation and i had to restart the runs twice. Following are the files I obtained after completion of mdrun (I am writing information of .xtc only, for .trr its same: *md_0_1.xtc = 0 to 100 ns* *new.xtc = 99.990 to 159.990* *v.xtc = 166.050 to 179.050* *traj-comp.xtc = 179.620 to 200.00 ns* Now I am surprised to see that the time frames from 159.990 to 166.050 are not written to any file. I have also checked the .trr and .xtc file with gmx check and found that time frames are incomplete after the follwoing command: gmx check -f new.trr Checking file new.trr trn version: GMX_trn_file (single precision) Reading frame 0 time 0.000 # Atoms 133688 Reading frame6000 time 159990.000 *WARNING: Incomplete frame: nr 6607 time 166060* Item#frames Timestep (ps) Step 660710 Time 660710 Lambda660710 Coords660710 Velocities660710 Forces 0 Box 660710 Now I am not sure to catenate the avaialble file or should i start the run again from 159.990 to 166.050? iF YES, WHAT WOULD BE THE COMMAND FOR THAT... With Regards Suniba -- 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.
