[gmx-users] Dump with trjconv - periodic coordinates

leafyoung81-group at yahoo.com leafyoung81-group at yahoo.com
Thu Jan 5 03:40:51 CET 2006

For the second, try shake?

Yang Ye

----- Original Message ----
From: Malin Bergenstråhle <malbe at kth.se>
To: gmx-users at gromacs.org
Sent: Thursday, January 05, 2006 12:26:39 AM
Subject: [gmx-users] Dump with trjconv - periodic coordinates


When I make a coordinate dump from a trajectory with
trjconv -dump to a .gro - file
I get a coordinate file where the coordinates are sometimes out of the 
periodic box.
Is this normal, or could there be a problem?

I use pbc=full and try to simulate an "infinite" polymer, covalently 
bonded over the periodic boundary.
I have (still) problems with atoms at the periodic boundaries causing 
simulation crash due to Lincs complaining about bond rotations.

Best regards,

gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list