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

[Justin Lemkul]

On 10/24/15 4:41 PM, gozde ergin wrote:
> 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.
>

Something about your physical model is unstable.  Perhaps the topology, run 
settings, etc.  The usual advice: 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

-Justin

>
> 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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>>
>>

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

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

==================================================