[gmx-users] printing coords ; energies

Jochen Hub jhub at gwdg.de
Thu Sep 4 15:19:28 CEST 2008

Omer Markovitch wrote:
> Dear All,
> I would like to consult you on the following two things:
> 1) I have a small, preanalysis, routine I would like to run each time a
> frame is written and added to the trajectory file.
> After some checking, I believe that, in the file "*stat.c*", the routine
> "*void write_xtc_traj(FILE *log,t_commrec *cr,
>       char *xtc_traj,t_nsborder *nsb,t_mdatoms *md,
>       int step,real t,rvec *xx,matrix box,real prec)*"
> is the routine actually printing each frame.
> Is this true or perhaps I've missed something?
> 2) Regarding energies - where are the energies stored? I mean the energy per
> type?

The energies of the energy groups (as defined in the mdp file) are
stored in the edr file (ener.edr by default).


> In which file & variable is this defined?
> I understand that these values are printed to the log file (usually named
> md.log), but I failed to locate the exact functions dealing with this.
> Thanks, Omer.
> Koby Levy research group,
> Weizmann Institute of Science.
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> ------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Dr. Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
Tel.: +49 (0)551 201-2312

More information about the gromacs.org_gmx-users mailing list