[gmx-users] empty energy file

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jul 6 07:50:25 CEST 2006

kobi wrote:
> Hello,
> I have got a little Problem here. Since I added the option "-t 2nd_equi.trr" to my grompp command to takeover all
> velocities from my equillibrated state, my energy file (full.edr) is created, but nothing is written to it any more.
> Could anybody tell me what I did wrong?
> My runs were aborted without any output from gromacs after approx 10^5 to 10^6 steps.
> the commands I used:
> grompp  -nice 1 -f full -o full -c after_2nd_equi.pdb  -p topol.top -n pull.ndx -t 2nd_equi.trr
> mdrun -nice 1 -v  -s full -e full -o full -x full -c after_full.pdb -g full.log -pi pull.ppa -po pullout.ppa -pd pull.pdo -pn pull.ndx
> nstenergy is set to 2500 in the full.mdp file I use for the simulation.

You look to be doing sensible things, and the suggestion made by Dallas 
is a good one. You can test for that kind of problem by doing a smaller 
number of steps (say 10^4) and seeing what output exists after 
successful termination.


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