From: TJ Piggot <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] Inconsistent shifts using multiple bonds type 6
Date: Tue, 06 Mar 2007 00:22:00 +0000
Hi Mark thanks for your reply,
I'm not sure the problem is that these restraints are inappropriate, but
the problem might be the sheer number. For example if i restrain a fairly
large number of atom distances (say 100 Calpha distances) to the same
length they are in the structure after minimisation and position restrained
MD then mdrun still crashes, even if i use a very weak force for the
restraint.
I have also been playing round trying to fix the problem and have noticed
from the mailing list that inconsistent shifts are seen when people are
using infinite systems and have not set pbc=full. I know i am not using the
kind of system but setting pbc=full does not result these problems that i
see when i use pbc=xyz. Is pbc=full reasonable to use for production runs
and does anyone know roughly how much slower it is (time is quite important
as i have a large system)
Thanks again
Tom
Inconsistent shift should only occur with infinite molecules,
or when distances between atoms connected by bonded
interactions exceed half a box dimension.
Is the latter the case for your system?
You can safely use pbc=full for production runs (I only noticed
recently this option is missing in the mdp option manual).
The performance difference should be a few percent.
Berk.
_________________________________________________________________
Live Search, for accurate results! http://www.live.nl
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php