[gmx-users] Extended trajectory

[Arik Cohen]

Hi,

I'll be most thankful if someone could tell me how to run a fragmented 
trajectory using only the mdrun command. As of now I'm using :

 while(SimuTime < SimTime)
    {
       ...
     system("tpbconv -s run.tpr -f run.trr -e run.edr -extend 1.0 -o 
run.tpr");
     system("mdrun -cpi run.cpt -cpo run.cpt -append -npme 0 -v -deffnm 
run");
     ....
    }

When I ran the above mdrun command alone, the run got stack

Thanks

Arik