[gmx-users] Segmentation fault in some windows of umbrella sampling

[Justin Lemkul]

On 10/23/15 11:38 AM, gozde ergin wrote:
> Dear users,
>
> I am doing umbrella sampling and using gromacs 4.6.
> I followed the Justin tutorial and generated 200 configurations on reaction
> coordinate.
> I faced segmentation fault error for 34 configurations (windows) but 166 of
> them run without any error.
> I thought maybe systems were not equilibrated enough so I run energy
> minimization step by using double precision, lower energy step and maximum
> force however I still get the same error.
>
> Do you have any idea about the reason?
>

Are the failing windows randomly throughout the reaction coordinate, or 
clustered in one region?  Do the simulations run in the absence of a biasing 
potential?  What is your system?

-Justin

-- 
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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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