AW: [gmx-users] Regarding trajectory file

[Rausch, Felix]

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: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] 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 <Mark.Abraham at anu.edu.au>
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
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