[gmx-users] Re: mdrun on GROMACS 3.3.1

Francesca Vitalini francesca.vitalini11 at gmail.com
Tue Aug 28 20:08:08 CEST 2012

Hi Sheeba,

with time I understood why it was happening. Check in the mdp file if you
still have the parameters to couple with the coarse grained file and
comment them. If they are present in the mdp file then mdrun looks for the
coarse grained file.

Hope this will be helpful


2012/8/28 Sheeba <sheeba.jem at gmail.com>

> Hi, I have been working on the reverse transformation and I had the same
> problem with mdrun generating the error:
> Can not open file:
> coarse.xtc
> However this happens only when I use mdrun from the modified 3.3.1 version
> without the '-coarse' option, which is similar to what Francesca vitalini
> had used:
> $MYGROMACSPATH/bin/mdrun -v  -s dynamin_dimer_PR1.tpr  -o
> dynamin_dimer_PR1.trr  -cpo dynamin_dimer_PR1.cpt -c dynamin_dimer_PR1.gro
> >From what I understand, the modified version is built to couple the CG
> structure with the transformed AA structure using the parameters listed in
> the input file. However after simulated annealing and releasing the
> restraints when we try to run a regular MD run, there is no need to couple
> with the CG structure and hence we ignore the '-coarse' option and mdrun
> crashes.
> Ideally once the restraints are released the resulting .gro file can be run
> with a newer version of Gromacs with the necessary updates to the itp files
> where applicable. This I have done for my system and I am able to
> successfully run a transformed AA system.
> However I also tried to find a work around to equilibrate the AA structure
> with the mdrun in the modified 3.3.1 version and this can be achieved by
> generating the tpr file for mdrun after removing the mapping section in the
> all-atom itp files and then using mdrun with the '-coarse' option
> mentioning
> the CG structure. This only gives an illusion that mdrun couples the CG
> structure but since there is no mapping section in the itp files it does
> not
> actually couple the CG structure and the resulting PE I get are similar to
> the PE for a regular AA system.
> This is however my observation and I would appreciate if the developers of
> the modified 3.3.1 version could check and confirm it.
> Sheeba
> -----
> Sheeba J. Irudayam
> Postdoctoral Researcher
> Department of Chemistry
> University of North Carolina at Chapel Hill
> isheeba[at]email.unc.edu
> --
> View this message in context:
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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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