[gmx-users] Flat-bottomed Restrain

[Salman Zarrini]

Ehsan,

That is just a single cylinder, or if you wish you can call it 5 identical
overlapping cylinders corresponding to each atom, but that still is just
one cylinder.
Actually you still have your original *.GRO of your system fed to grompp by
-c flag, the reference.gro edited that way is just a reference coordinate
by which you dictate the desired molecule to move around the axes at (3.0,
3,0) as much as 1.5 nm while the molecule is free to move along the Z as
much as it likes.

Regards,

Salman Zarrini


On Tue, Jul 16, 2019 at 1:03 PM 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
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-request at gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>