RMSF is calculated for the atoms or groups you specify in your selection
string. If you say, e.g. "protein and name CA" you will get all C alphas in
the protein(s) in your system. See here
http://manual.gromacs.org/documentation/5.1/onlinehelp/selections.html

On Thu, May 17, 2018 at 10:18 AM, Sampurna Mukherjee <
sampurnamukherjeebiol...@gmail.com> wrote:

> Hi gmx-users,
>                               There are a few things I wanted to know:
>
>    1.  For RMSF calculations, which atoms are used when I am calculating
>    RMSF for a group specified in the index?
>    2. For gmx mdmat , for 2 protein chains taken together i.e using the
>    Protein group ,  "smallest distance between residue pairs" implies the
>    smallest distance over the trajectory between say the first and the 15th
>    residue.Yes?
>    3. Which atoms are being considered for calculation of smallest
>    distances?
>
>
>
> Regards,
> Sampurna
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