[gmx-users] constraints bond length vari by 10%

[Mark Abraham]

----- Original Message -----
From: Sebastian Waltz <sebastian.waltz at physik.uni-freiburg.de>
Date: Tuesday, June 15, 2010 22:09
Subject: [gmx-users] constraints bond length vari by 10%
To: gmx-users at gromacs.org

> Hi all,
> 
> I added constraints on some bonds in my system by adding 
> 
> [ constraints ]
> ;ai   	aj	type	distance
>    40	41	1	0.1230
>    47	48	1	0.1230
>    54	55	1	0.1230
>    61	62	1	0.1230
> 
> to me top file (CO double bonds) and in the mdp file 
> 
> constraints         
> =  none
> 
> . I thought this should more or less fix my bond lengths.
> Nether the less the bond lengths vary by 10%. Did I make
> something or is it quite normal? What would be the way to
> fix the bond length so that they vary only by ca. 1%.

You're using the right approach, but you've probably not put your [constraints] directive in the right [moleculetype], or used the wrong .top/.itp/.tpr file at some point.

Mark

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