[gmx-users] Segmentation fault in some windows of umbrella sampling
gozdeeergin at gmail.com
Sat Oct 24 18:37:47 CEST 2015
It is totally random. My system is 50 1-decanol2,4,8trimethyl molecules
covered on 512 water molecules,
Before, I did the umbrella sampling by using 1_decanol2468tetramethyl and
1-decanol as organic molecules and I did not get any error like this. Do
you have any idea?
On Fri, Oct 23, 2015 at 7:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> I faced segmentation fault error for 34 configurations (windows) but 166
>> 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 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
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