[gmx-users] trjconv woes (broken molecules)

Ignacio Fernández Galván jellby at yahoo.com
Tue Feb 19 19:28:35 CET 2013

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.

I can't find anything that works reliably, can anybody help me?

Thank you

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