[gmx-users] Regarding trajectory file

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Wed Jan 18 13:17:37 CET 2012

On 18.01.2012 07:31, 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

In the directory of the xtc file, the (2'nd) command

  $>  mkdir GRO
  $>  trjconv -noh -novel -skip 1 -sep -nzero 4 -o GRO/out.gro

will save every single frame of your simulation in
a .gro file into a subdirectory GRO/

If you don't wan't every single frame, use
"-skip 2" in the above option to get every
second frame.


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