[gmx-users] gmx dos - Possible bug on 5.0.6

[Justin Lemkul]

On 8/25/15 5:03 PM, Marcelo Depólo wrote:
> 2015-08-25 17:29 GMT-03:00 David van der Spoel <spoel at xray.bmc.uu.se>:
>
>> On 25/08/15 18:24, Marcelo Depólo wrote:
>>
>>> Hi all!
>>>
>>> I've been running gmx dos (version 5.0.4) in some trajectories with the
>>> following:
>>>
>>> echo BEN | gmx_504 dos -s ben.DOS.tpr -f ben.DOS.trr -g ben.log -dos
>>> dos.xvg -vacf vacf.xvg -mvacf mvacf.xvg
>>>
>>> and it runs just fine. But when I run the same line with 5.0.6, I get:
>>>
>>> That means the results from previous versions may not have been what you
>> thought they would be. What are you trying to accomplish? gmx dos does not
>> do anything useful with an index file.
>>
>
> I am calculating Cv from DoS simulations. Still, I haven't use any index
> file in my line. I used precisely the same one as above. I have checked
> both gmx_dos.c and there is a new code implemented on 5.0.6, exactly in the
> part of counting atoms (if I am not mistaken).
>

Indeed, this new function is causing the problem.  Please upload a minimal test 
case to Redmine.

-Justin

>>
>>>
>>>
>>>
>>>
>>> *-------------------------------------------------------Program gmx_506,
>>> VERSION 5.0.6Source code file:
>>>
>>> /home/marcelodepolo/Downloads/BACKUP-softwares/gromacs-5.0.6/src/gromacs/gmxana/gmx_dos.c,
>>> line: 93Fatal error:Index contains atom numbers larger than the topology*
>>>
>>> Did anyone already come across this?
>>>
>>> Cheers!
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>> --
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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

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