[gmx-users] trjconv for pbc

[Tsjerk Wassenaar]

Hi Blake,

Centering on the solute should help.

Cheers,

Tsjerk


On Sat, Nov 2, 2013 at 3:55 PM, rankinb <rankinb at purdue.edu> wrote:

> Hi all,
>
> I am trying to use trjconv to remove PBC.  More specifically, I would like
> to extract the coordinates of all the water molecules within a certain
> distance of a single solute molecule.  However, I have been unsuccessful in
> doing so, even after following the guidelines on the GROMACS website
> (
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> ).
>
> Here are some of the things I have tried. First, I extracted the indices of
> the water molecules of interest using g_select and used trjconv to extract
> the coordinates from the .gro file.  Then I used trjconv -pbc mol on the
> resulting .gro file.  The problem is that some of the water molecules are
> on
> opposite sides of the box.
>
> Does anyone have any suggestions?
>
> Thank you very much,
> Blake
>
> PhD Candidate
> Purdue University
> Ben-Amotz Lab
>
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-- 
Tsjerk A. Wassenaar, Ph.D.