[gmx-users] About gromacs run...

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jan 2 11:35:03 CET 2010

Hi Henry,

Doing so will give you a loss of precision and you won't have continuity for
the thermo/barostat. You would be better off using tpbconv -extend or
tpbconv -until, with the .tpr, .edr, and .trr as input. That will also save
editing files.

Hope it helps,


On Sat, Jan 2, 2010 at 10:37 AM, Henry Yang <henryynag at yahoo.com> wrote:

> Dear users,
> Happy new yera to all.
> I have just a very simple query..
> I am running a simulation for 100 ns. I have decided to run it by 10 ns
> step of each. In every run, the gromacs generated confout.gro file, the
> traj.trr, traj.xtc, md.log , ener.edr file, state.cpt etc. The next time
> when i run the simulation for the next 10 ns , I have edited the em.mdp file
> and just change the tinit to the last time that i was run and the nsteps to
> 5000000 for 10 ns.. And the command i used for grompp is ...
> grompp -f em.mdp -c confout.gro -p topol.top -o topol.tpr
> And then it will generate the topol.tpr file. and the command is then
> mdrun
> My question is is that oaky ... or I have to use any more file in the
> grompp command like that traj.trr or state.cpt for tracking velocity??
> Thnx...
> /Henry
> Biochemistry.
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Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
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