Hi Berk,
Thanks for your reply. Yes the latter is the case in my system so i will
use pbc=full or remove these 'bonds' that i know will be greater than half
of a box dimension
Thanks again
Tom
--On Tuesday, March 06, 2007 10:52:52 +0100 Berk Hess <[EMAIL PROTECTED]>
wrote:
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.
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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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