[gmx-users] fast rerun in order to get an energy

Jeffery Perkins Jeffery.Perkins at ufv.ca
Fri Jul 9 19:04:13 CEST 2010

I'm no expert but try a rerun, it will allow you to get at least the potential energies for each frame in your trr or xtc file, I've never been interested in kinetic for my reruns and as such am unsure how that would work though it should be possible.  For this you'll need to build a slightly different mdp file with at least the following options (other stuff should be the same as in your initial run of this system)

nsteps = 0
nxtenergy = 1

I usually turn the trr or xtc that I need to rerun into a gro file for input using
trjconv -f traj.trr -o out.gro -ndec 3

You then need to grompp this new mdp file something like:
grompp -f rerun.mpd -p topol.top -c out.gro

and run an mdrun with the -rerun option turned on.

mdrun -rerun traj.trr

this should give you the energies at each frame in the normal ener.edr file used by g_energy

May have missed something but this should be a good place to start looking, best of luck,

Jeffery Perkins

Magdalena <madlen12 at o2.pl> wrote:

Hi, i will be grateful for any clue.

Is it possible to extract an energy from finished trajectory? In my case the trajectory wasn't leading with flag e so it's obvious that I haven't got any edr files.
I know that in log file there is some information about energy but I would like to have it in one file. My trajectory is quite long so that why I wouldn't like to start calcultations from the beginnig in order to achieve right files. If somebody had a similar situation then would be so kind and instruct me in right direction?
Thanks in advance

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