[gmx-users] Mixed Solvent (H2O/CH3CN)

[Justin Lemkul]

On 3/19/15 8:29 AM, Debashis Sahu wrote:
> Dear Gromacs users,
>                               I have faced a problem recently for the NVT
> simulation of a small organic receptor in acetonitrile solvent. I got the
> following errors even varying the box sizes as well as the number of
> solvent.
>
> starting mdrun 'Giant Rising Ordinary Mutants for A Clerical Setup in water'
> 50000 steps,    100.0 ps.
> step 11500, remaining runtime:   135 s          Segmentation fault (core
> dumped)
>
> To examine the effect of role acetonitrile, I have also used the mixed
> solvent box(water and acetonitrile). I have observed the similar problem.
> But it is interesting that when I have used simple water solvent box the
> simulation running smoothly. Can anyone help me to overcome this problem.
>

If every run with acetonitrile fails, you probably have a problem in the 
acetonitrile topology.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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