[gmx-users] Density of States syntax question

[Marcelo Depólo]

Hi!

That's an bug that was not corrected yet for the 5.1 version. Its somehow
linked to a safety measure that went nuts. The issue was already directed
to the admins.

Try to use 501 version. For me, it works just fine.

Cheers!

2016-05-31 10:59 GMT-03:00 Chapman, Christopher W. <chapmancw at ornl.gov>:

> Hello all,
>
> I am new to Gromacs, so I apologize if this is a trivial question. I'm
> running a Gromacs tutorial (found at
> https://github.com/wesbarnett/gromacs-tutorials/tree/master/1_tip4pew_water)
> using Gromacs v5.1.2, and I was trying to get the Density of States from
> the production run. When I type in the following:
>
> gmx dos -f prd.cpt -s prd.tpr
>
> and choose any of the Groups listed (0 for 'System', 1 for 'Water', 2 for
> 'SOL'), I get the following:
>
> Program gmx dos, VERSION 5.1.2
> Source code file:
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/gmxana/gmx_dos.c, line: 94
>
> Fatal error:
> Index contains atom numbers larger than the topology
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
> What exactly does this mean, and how do I go about fixing this (assuming
> it's possible)? Also, is it possible to get the density of states for each
> individual atom (Oxygen and Hydrogen, in this case), or is it only
> available for the molecule as a whole?
>
> Sincerely,
>
> Chris W. Chapman
> Computational Reactor and Medical Physics Group
> Nuclear and Radiological Engineering
> Georgia Institute of Technology
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-- 
--
Marcelo Depólo Polêto
MSc Cell and Molecular Biology - UFRGS (Brazil)
Group of Structural Bioinformatics - Room 202
Center of Biotechnology - UFRGS
Phone: + 55 51 3308-7770