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

[Sebastian Waltz]

Hi Mark,

what I have written in the .top you can see in my first
massage. I actually don't know what to write what and in
which .itp/.tpr file I have to add something and I also
can't find something in the Internet. The documentation for
the constraints is just bad.

Thanks

Sebsatian      

On Wed, 16 Jun 2010 09:05:20 +1000
 Mark Abraham <mark.abraham at anu.edu.au> wrote:
> 
> 
> ----- 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
>