[gmx-users] looping job: time not updating

Justin Lemkul jalemkul at vt.edu
Fri Mar 14 00:34:53 CET 2014

On 3/13/14, 7:29 PM, gromacs query wrote:
> Hi All
> Though its mentioned here how to restart jobs:
> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
> but I tried to run something like this (by scripting) but copying here how
> script is looping jobs:
> #stage 1
> grompp -f npt.mdp -c conf_1ns.gro -t state_1ns.cpt -p topol.top -o npt2.tpr
> -n index.ndx
> mdrun -s npt2.tpr -o traj_2ns.trr -e ener_2ns.edr -c conf_2ns.gro -g
> md_2ns.log -cpo state_2ns.cpt
> #stage2
> grompp -f npt.mdp -c conf_2ns.gro -t state_2ns.cpt -p topol.top -o npt3.tpr
> -n index.ndx
> mdrun -s npt3.tpr -o traj_3ns.trr -e ener_3ns.edr -c conf_3ns.gro -g
> md_3ns.log -cpo state_3ns.cpt
> When I look in any log file it always start time at 0, what I have missed
> here?

You're re-using the same .mdp file, which probably specifies "tinit = 0" (or 
does not specific tinit at all, so it defaults to zero) so time starts over.

The only reason to invoke grompp between runs is if you are changing .mdp 
settings (restraints, output frequency, etc).  Otherwise, you need tpbconv, as 
stated on the page linked above.



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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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