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

Marcelo Depólo marcelodepolo at gmail.com
Tue Aug 25 23:03:15 CEST 2015


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).

>
>>
>>
>>
>>
>> *-------------------------------------------------------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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-- 
Marcelo Depólo Polêto
Group of Structural Bioinformatics - Center of Biotechnology
Student of MSc Cell and Molecular Biology - UFRGS (Brazil)
B.Sc. Biochemistry - University of Viçosa (Brazil)


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