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

[gozde ergin]

Also I tried the run these windows by using different computers and
different Gromacs versions (5.0 and 5.1) however I always got the same
segmentation fault error.


On Sat, Oct 24, 2015 at 6:37 PM, gozde ergin <gozdeeergin at gmail.com> wrote:

> Hi Justin,
>
> 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?
>
> Bests
>
>
> 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
>>> 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
>>
>> --
>> ==================================================
>>
>> 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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>
>