[gmx-users] Separate structure from box

Wes Barnett w.barnett at columbia.edu
Tue Mar 20 12:17:41 CET 2018

On Tue, Mar 20, 2018 at 2:30 AM, rose rahmani <rose.rhmn93 at gmail.com> wrote:

> Hi,
> I want to extract a structure in a box, i mean i want to extract a sheet
> from the box of solution, because i dont have any separated .gro file from
> my sheet. How can i do that?

Try creating an index file using "gmx make_ndx" to create an index group
containing just the atoms you want. Then use "gmx trjconv" to output a file
only containing that group. See the "-h" flag for both of those commands.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

More information about the gromacs.org_gmx-users mailing list