[gmx-users] A fragmented trajectory
Mark.Abraham at anu.edu.au
Tue Oct 20 02:08:32 CEST 2009
Arik Cohen wrote:
> Dear users,
> I'll be most thankful if someone could give me an example as how to
> restart a MD simulation that is been fragmented into several sections. I
> have tried several flags according to the manual with no success. Every
> time a different problem emerges, i.e. either the simulation get stuck
> and a massage such as, npme is different for the current and previous
> run, or .tpr file can not be found and so on.
> The general spirit of the simulation is as follows:
> void ScaffHandler::MD(double SimTime)
> system("grompp -f MDP/runmd.mdp -p topol.top -c pr.gro -o run.tpr");
> system("mdrun -v -deffnm run");
> while(SimuTime < SimTime)
> system("mdrun -cpi run.tpr -v -deffnm run");
This command is malformed. -cpi expects a checkpoint file, and you're
supplying a run input file. See mdrun -h.
> SimuTime += 0.001;
> Thanks allot
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