Reruns MUST use trr files. On Jul 9, 2010, at 19:04, "Jeffery Perkins" <[email protected]> wrote:
> 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 <[email protected]> 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 > > -- > gmx-users mailing list [email protected] > http://lists.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list [email protected] > http://lists.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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list [email protected] http://lists.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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
