[gmx-users] Inconsistent shifts using multiple bonds type 6

TJ Piggot t.piggot at bristol.ac.uk
Tue Mar 6 13:44:16 CET 2007

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


--On Tuesday, March 06, 2007 10:52:52 +0100 Berk Hess <gmx3 at hotmail.com> 

>> From: TJ Piggot <t.piggot at bristol.ac.uk>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at 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
t.piggot at bristol.ac.uk
University of Bristol, UK.

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