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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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