[gmx-users] Not able to continue with Equilibration

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 30 14:26:05 CEST 2012

francesca vitalini wrote:
> 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?

Where did you obtain this version of Gromacs?  You're not using an official 
version, so you're not likely to find its documentation in the usual places and 
it's very hard for this community to help you using a modified version of 
antiquated software.  You're more likely to have luck contacting whoever created 
these modifications for help, since potential problems with code stability and 
performance are likely best addressed by those who made the modifications. 
Perhaps they are members of this list, but contacting them directly is probably 
a better approach.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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