[gmx-users] Flat-bottomed Restrain

[Salman Zarrini]

Hi Ehsan,

Here is how I understood and would implement the flat-bottom potential;

Just suppose you intend to confine a molecule with five atoms in a cylinder
with radius of *\rho = 1.500* nm and axes positioned at *x = 3.000 and y =
3.000 nm* parallel to the Z.
First you need a posre.rho.itp in which the restrain's properties are
defined;
posre.rho.itp
;Z - Cylinder:
[ position_restraints ]
; i funct   g_z    \rho(nm)   K(kJ mol-1 nm-2)
  1   2      8       *1.500*       3500
  2   2      8       *1.500*       3500
  3   2      8       *1.500*       3500
  4   2      8       *1.500*       3500
  5   2      8       *1.500*       3500

Similar to all other restrains the posre.rho.itp should come in the end of
[moleculetype] section of the desired molecule, for instance using #ifdef
... #endif to be called later in mdp file.

You still need one more file to be fed to grompp using -r as reference
positions, as Mark pointed out;
;reference.gro
Reference
*127972*
   1AMNA   H14    *1*   *3.000   3.000*   4.325   ;(no confinement along
the Z)
   1AMNA   C11    *2*   *3.000   3.000*   3.789
   1AMNA   H12    *3*   *3.000   3.000*   2.405
   1AMNA   H13    *4*   *3.000   3.000*   5.608
   1AMNA   C10    *5*   *3.000   3.000*   4.390
   ... (rest of the unrestrained atoms)
   ... (rest of the unrestrained atoms)
   ... (rest of the unrestrained atoms)
   ... (rest of the unrestrained atoms)

I hope it works!

Cheers,
Salman Zarrini


On Tue, Jul 16, 2019 at 4:58 AM 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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