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

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 9 19:02:25 CEST 2010

Magdalena 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

You didn't get an .edr file at all?  Did you specify nstenergy > 0 in the .mdp 
file?  It seems odd that you didn't get anything.  The .edr file is a standard 
output file, there is no need to specify any flag to cause it to be written.

> 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

You can pass your trajectory file to mdrun -rerun and it will recalculate the 



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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