[gmx-users] Reference atoms for gmx mdmat and gmx rmsf

[Sampurna Mukherjee]

Thanks for the selection help. However, I wanted to understand what is the
default selection performed by GROMACS is no specification is given for
RMSF calculation, i.e suppose only a protein group is specified.

On Thu, 17 May 2018, 15:05 Joe Jordan, <e.jjordan12 at gmail.com> wrote:

> 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 <
> sampurnamukherjeebiology at 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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>
> --
> Joe Jordan
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