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

[Joe Jordan]

Try running it with no index file and see what happens =)

On Thu, May 17, 2018 at 11:53 AM, Sampurna Mukherjee <
sampurnamukherjeebiology at gmail.com> wrote:

> 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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-- 
Joe Jordan