[gmx-users] Density of States syntax question

Chapman, Christopher W. chapmancw at ornl.gov
Tue May 31 15:59:43 CEST 2016

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?


Chris W. Chapman
Computational Reactor and Medical Physics Group
Nuclear and Radiological Engineering
Georgia Institute of Technology

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