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. <chapma...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- -- 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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.