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

[Berk Hess]

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 12:44:16 +0000

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

You should remove those bonds, or make the box larger.
pbc=full will work, but the distance vector will change to different
periodic images when an "inter"-molecular periodic image distance
becomes shorter than the true intramolecular distance.

I assume your molecule is properly connected by normal bonds.
A real fix would then be adding
i!=F_HARMONIC &&
to the if statement on line 272 of src/gmxlib/mshift.c
and recompiling Gromacs, such that the harmonic potentials
are not put into the graph.

Berk.

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