[gmx-users] Not able to continue with Equilibration

francesca vitalini francesca.vitalini11 at gmail.com
Fri Mar 30 11:18:01 CEST 2012

Dear Mark,
Thank you for your answer. I'm trying now with the position restraints
and see what happens.
However, another question came up to my mind in the mean time. I'm
using GROMACS 3.3.1 (version with mapping for reverse transformation,
I have been posting on it before) and for the mdrun the flag -coarse
is required. From the mdrun -h help, the -coarse flag resulted to be a
generic trajectory, so I assumed it was needed for the names of the
atoms or something similar. However, trying to run the nvt.mdp with
the original coarse grained file specified for this flag, resulted in
the simulation not dying at the very first steps.
 I'm not sure if it will work out eventually ( the 20 ps simulations
is supposed to finish in 12 hours, which is still kind of worrying
despite my system being pretty big) but definitely told me that the
-coarse flag might be of fundamental importance.
Unfortunately I couldn't find any more detailed documentation about it.
Could anyone explain to me what it does or point me to where to find
the related documentation?
Thank you very much

2012/3/30 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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
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Francesca Vitalini

PhD student at Computational Molecular Biology Group,
Department of Mathematics and Informatics, FU-Berlin
Arnimallee 6 14195 Berlin

vitalini at zedat.fu-berlin.de
francesca.vitalini at fu-berlin.de

+49 3083875776
+49 3083875412

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