[gmx-users] A fragmented trajectory

[Mark Abraham]

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.

Mark

>     SimuTime += 0.001;
> 
>     ...
>      }
>  ....
> }
> 
> Thanks allot
> 
> Arik
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