Or you could use trjconv in a little script to convert the snapshots you like to .pbd. Use the -b and -e flags to choose the respective time points.
Also see http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts for the use trjconv non-interactively. Good luck. Von: [email protected] [mailto:[email protected]] Im Auftrag von aiswarya pawar Gesendet: Mittwoch, 18. Januar 2012 07:53 An: Discussion list for GROMACS users Betreff: Re: [gmx-users] Regarding trajectory file You can write this on VMD forum. Anyways you can try by doing this in the Tcl console- set sel [atomselect top "solvent"] $sel get {x y z} This would give you the coordinates of the solvent, for your purpose you got to iterate so as to get for each time step. Aiswarya SERC Dept, IISc Bangalore On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham <[email protected]> wrote: On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote: Dear All, I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using VMD or any other viewer. You're unlikely to get help for non-GROMACS software on this mailing list. Check out manual section 7.4 for clues on what GROMACS tools might help, and then section 8 and appendix D for more details. Mark -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
