[gmx-users] Flat-bottomed Restrain

[ehsan shahini]

Thank you so much for your response. For my first question, are you
suggesting using a command like this:

 gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -r
small_molecule.gro -o md.tpr

This command, however, results in a warning and a fatal error:

WARNING 1 [file unknown]:
  The number of atoms in small_molecule.gro (59) does not match the number
of atoms in
  the topology (54073). Will assume that the first 59 atoms in the topology
  and small_molecule.gro match.


fatal error:

Can not invert matrix, determinant is zero

Even though I changed the topology and npt.gro in a way that the first 59
atoms were the atoms of the small molecule the error insisted.

Formerly, I used -r npt.gro and used flat-bottomed restrain on a single
atom and it worked for that particle. So what does "-r" flag do? I read the
manual but there is not much information on it.

Kind regards,

Ehsan
On Tue, 16 Jul 2019 at 13:28, Mark Abraham <mark.j.abraham at gmail.com> wrote:

> Hi,
>
> On Tue., 16 Jul. 2019, 10:32 ehsan shahini, <ehsan.shahiny at gmail.com>
> wrote:
>
> > Dear all,
> >
> > 1. I need to restrain a small molecule in a region (cylindrical) and I
> want
> > to restrain all of its atoms in that region. The best tool is
> flat-bottomed
> > restrain but it only restrains individual atoms in their corresponding
> > regions and not all the atoms in a single region.
> >
> > Hence, if I want to change the main code related to flat-bottomed where
> can
> > I find it?
> >
>
> No need. Use grompp -r to restrain the position of each atom to the same
> position that is the centre of the desired region.
>
> Another question
> >
> > 2. Can we introduce virtual sites in Gromacs which are static and defined
> > by the user via the XYZ coordinates of them?
> >
>
> No, but you can have frozen particles that have whatever interactions that
> you choose.
>
> Mark
>
>
> Kind regards,
> >
> > Ehsan
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