[gmx-users] Difference between residue (r) and residue index (ri) when selecting residue groups?

[Justin Lemkul]

On 8/15/19 12:16 PM, Dhaniram Mahato wrote:
> r will select all atoms without hydrogens.
> ri will select all atoms including all hydrogens too.

This is not correct. GROMACS has default groups with and without hydrogens.

r selects based on the actual residue number. ri is supposed to select 
based on *index* - a zero-based residue numbering. In practice, however, 
they seem to have identical functions, which seems like a bug (I just 
tried it).

The code seems correct, but the output is not consistent with what one 
would expect.

-Justin

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Justin A. Lemkul, Ph.D.
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