[gmx-users] trjconv for pbc

[rankinb]

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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