[gmx-users] trjconv woes (broken molecules)

Justin Lemkul jalemkul at vt.edu
Tue Feb 19 19:33:49 CET 2013

On 2/19/13 1:28 PM, Ignacio Fernández Galván wrote:
> Hi all,
> I have a simulation with a frozen molecule which stays around the origin, and a number of solvent molecules with pbc. Due to the way the simulation cell is defined, with a corner at the origin, by default my frozen molecule appears broken, a piece on every corner of the box, and I want it whole (and if possible centered).
> In a simple world, I'd use trjconv with -pbc res (or mol) and -center, but of course, that doesn't work when initially the molecule is broken, as its center of mass is in a meaningless position. I can use -pbc atom, but then the solvent molecules get broken.
> So I assume I have to use a multi-step conversion, and I have to first get a whole molecule. But I tried -pbc whole and -pbc cluster and they don't make any difference.

First use:

trjconv -trans x y z -pbc mol

This will allow you to reposition the elements of your system such that you have 
an intact structure at the origin.  Then use the structure created as your new 
reference structure for further trjconv iterations (removing jumps, making 
molecules whole, etc).



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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