[gmx-users] empty energy file

kobi kobi17 at gmx.de
Thu Jul 6 18:50:50 CEST 2006

Hi Mark, hi Dallas,

I'll try your suggestion.

Thanks a lot!!

Mark Abraham schrieb:
> 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.
> Mark
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