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

[gozde ergin]

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
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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