[gmx-users] A fragmented trajectory

Arik Cohen acohen at biochem.duke.edu
Mon Oct 19 23:02:44 CEST 2009

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");
     SimuTime += 0.001;


Thanks allot


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