Extremely helpful! Thanks On Wed, Feb 6, 2019 at 3:29 AM Fotis Baltoumas <fbaltou...@biol.uoa.gr> wrote:
> Hello Tim, > > In GROMACS trajectories, the simulation time is normally saved alongside > the coordinates in the trr and xtc files as produced by GROMACS itself. > That's how the various analysis tools can understand time when it is > required. > > However, NAMD does not save the simulation file in the DCD format; that > information is contained exclusively in the logs. Therefore, when you > converted your trajectory to the trr format (I assume you used catdcd), > you just saved coordinates, not timesteps. > > To add timestep information in your trajectory you should, prior to > analysis, perform another manipulation with trjconv, using the "-t0" and > "-timestep" options properly. > > > For example, if you have a file called "traj.trr" that has 5000 frames, > starting at 0 ps with each frame recorded every 10 ps, you should do > something like the following : > > trjconv -f traj.trr -s structure.pdb -o traj_time.xtc -t0 0 -timestep 10 > > (I assume you use Gromacs 4.x or earlier, since you reference "g_msd" > instead of "gmx msd", otherwise, use "gmx trjconv"). > > Then use the result, traj_time.xtc as input for g_msd. > > Hope this helps, > > Fotis Baltoumas > > > -- > Fotis A. Baltoumas, Bsc, Msc > Phd Candidate, Bioinformatics Postgraduate Programme > Section of Cell Biology and Biophysics > Department of Biology > National & Kapodistrian University of Athens > Panepistimiopolis, Athens 157 01, GREECE > -------------------------------------- > > email : fbaltou...@biol.uoa.gr > http://biophysics.biol.uoa.gr > http://bioinformatics.biol.uoa.gr > Tel.: +30 2107274876 > Mob.: +30 6979258570 > > > > --- > This email has been checked for viruses by Avast antivirus software. > https://www.avast.com/antivirus > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
