[gmx-users] Flat-bottomed Restrain

[Mark Abraham]

Hi,

He's set the reference positions (in the -r file), rather than changing the
initial positions (with the -c file).

Mark

On Tue., 16 Jul. 2019, 19:03 ehsan shahini, <ehsan.shahiny at gmail.com> wrote:

> 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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