[gmx-users] Re: gmx-users Digest, Vol 17, Issue 39

Malin Bergenstrahle malbe at kth.se
Mon Sep 12 19:01:16 CEST 2005


Message: 7
Date: Mon, 12 Sep 2005 23:38:01 +0800
From: Yang Ye <leafyoung81-group at yahoo.com>
Subject: Re: [gmx-users] constraints and pbc=full
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4325A0D9.6030008 at yahoo.com>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Malin Bergenstrahle wrote:

 >> Hi,
 >> I am trying to simulate a system of infinite cellulose chains by using
 >> pbc=full.
 >> As far as I have understood from the list this option cannot be used
 >> together with any bond constraints. Is this correct? It is possible to
 >> run simulation with the constraints, but I guess something becomes 
 >> This seems to be a problem for me, because I have a couple of
 >> hydrogens that seem to get unreasonable high energy and start
 >> rotating; i.e. I would like to use constraints=hbonds.

 >You may use CVS version for pbc=full with lincs. SHAKE is not
 >implemented yet.

Ok, I am not sure if I know what you mean with CVS version? I have 
installed Gromacs 3.2.1, does that work or do I have install something else?


 >> If anyone has any suggestion about what I could do instead of
 >> constraining the h-bonds, or any idea about what could possibly be
 >> wrong I would be mostly grateful.
 >> /Malin
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