[gmx-developers] How to utilize the index file in code? GROMACS 4.6.3

Mark Abraham mark.j.abraham at gmail.com
Tue Nov 26 18:39:39 CET 2013

grompp accepts the index file and does all of the checking - mdrun just
gets a vector of 0 or 1 in the .tpr file according to which atom is in
which type of group. You should not need to get involved there, though,
because the .mdp options user1-grps and user2-grps are intended to suit
what your purpose sounds like. grep for User1 and cU1 to see how to get at
the resulting data structures.


On Tue, Nov 26, 2013 at 2:44 PM, Jheng Wei Li <lijhengwei at gmail.com> wrote:

> Hello, all
>   I am passing an index file chopping atoms into several subgroups, and
> I want to utilize this information in minimize.c!
> How do I recall index information in minimize.c?
> Please give me some advice or which part of code should I take a look to
> mimic its format!
> JhengWei Li
> Institute of Atomic and Molecular Sciences,
> Academia Sinica, Taipei 106, Taiwan
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