[gmx-users] Flat-bottomed Restrain

[ehsan shahini]

Dear Salman,

Thanks for the reply. For the first part, you are defining 5 cylinders with
a radius of 1.5. And, I'm not sure about your suggestion for editing the
.gro file in that particular manner since there is another option (function
3,4,5) for restraining atoms in a layer. But you are changing the x and y
coordinates of the atoms.

On Tue, 16 Jul 2019 at 19:36, Salman Zarrini <salman.zarrini at gmail.com>
wrote:

> 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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