[gmx-users] trjconv - more than one box

Justin Lemkul jalemkul at vt.edu
Thu Jan 3 12:21:57 CET 2013

On 1/3/13 5:09 AM, Weingarth, M.H. (Markus) wrote:
> Dear Gromacs users,
> I was wondering if one can use trjconv to get a .pdb file which shows more than one box?
> Just like the "genconf -nbox" command but with trajectories?

genconf has an option called -trj that sounds like it might do what you want, 
but I've never tried it.  Otherwise, you can script the process you want with 
multiple trjconv and genconf steps:

1. Use trjconv to split frames into separate coordinate files
2. Loop over coordinate files to run genconf -nbox
3. Use trjconv to reassemble a new trajectory from all the frames from step 2



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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