[gmx-users] Not able to continue with Equilibration

[Mark Abraham]

On 30/03/2012 8:39 AM, francesca vitalini wrote:
> Thank you Justin for your answer. I'm trying to add the position
> restraints to my protein, but I have a problem. My topology is made of
> a chain repeated twice and if I want to build the position restraints
> through genrestr from a gro file, the numeration of the atoms would
> put the 2 chains sequentially one after the other, but then the index
> would be out of bounds;

As genrestr -h and the manual tells you (and as was discussed on this 
list a day or two ago), [position_restraints] apply to all copies of 
that [moleculetype]. So use genrestr on the first molecule only and you 
will have position restraints for both molecules for the price of one.

>   if I try to generate the topology from x2top
> it has been taking more than 6 hours and hasn't finish yet. If instead
> I try to use the posre.itp built from pdb2gmx I still have the LINCS
> warnings, even after changing rlist, rcoulomb and rvdw to 1. Any ideas
> on a faster way to add my position restraints or how to solve the
> LINCS error? Thank you very much.

Follow the advice here 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up

Mark