[gmx-users] Problem regarding Simulation

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 2 13:02:54 CET 2011

madhumita das wrote:
> Hi GROMACS users,
>             I have generated .prmtop and .inpcrd files using xleap 
> module of AMBER for a  single chain of a membrane protein molecule 
> containing a modified residue. After that I have converted those files 
> into .gro,.top ,em.mdp and md.mdp files with the help of acpype.py. But 
> using the md.mdp file for simulating that protein in waterbox without 
> membrane produces following error:
>   Step6: Water molecule starting at atom 5486 can not be settled.
> And this error occurs severally.

Errors like these typically indicate insufficient minimization or equilibration, 
or that your .mdp settings produce an unstable simulation.  Since you haven't 
provided any of these details, it's hard to say what the real reason is.

I'd point you to the Gromacs website to find the workflow for diagnosing the 
problem, but unfortunately the website seems to be down.  Do check it later and 
search for the term "blowing up" - you will find possible solutions there.



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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