Hi, Good initiative, but unfortunately mdrun -rerun is unfit for pretty much anything connected with the velocities. See https://redmine.gromacs.org/issues/1868 for the gory details.
The potential energy should be fine (unless you are introducing a periodicity artifact in how you are using trjconv), but why are you involving trjconv at all? gmx mdrun -rerun prdv.trr works. Mark On Tue, Jan 30, 2018 at 10:37 AM dodia <do...@mpip-mainz.mpg.de> wrote: > Dear gromacs users, > > I am new user and trying to learn about the software by running simple > water box simulations. I did a 15ns NVT simulation of around 80 water > molecules (after 1.5ns+1.5ns of NVT & NPT equilibration) at 300K and the > resultant data seemed reasonably accurate wrt density and average > temperature. Now I tried to extract 50 frames from the trajectory and > stored them in a .gro file (with positions+velocities) and tried to use > mdrun -rerun to crosscheck energies, but in the resultant log file, the > temperature varies around 7000K, potential energy becomes positive and > other values go haywire. Can anyone help me with this issue? I used the > following commands after production calculation: > > > echo 1 | gmx trjconv -f prdv.trr -s prdv.tpr -vel -dt 100 -box 1.32 1.32 > 3.5 -o frame.gro > gmx mdrun -s prdv.tpr -rerun frame.gro -g test.log > > prdv is the file suffix for production simulation. prdv.trr contains all > the positions, velocities and forces at every 1.5ps > > Best Regards, > Mayank Dodia > -- > 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.
