[gmx-users] Is it possible to use both Gromacs pre-defined potential as well as tabulated potential simultaneously ?

Tue Mar 13 18:54:01 CET 2018

Hi,

I already suggested where to go and find the answer, but you looked
somewhere else... The PDF you linked is kindly contributed by another user,
but not official. Anyway, apparently my memory is wrong and you can't do
what you want. From the reference manual:

If you want to have different functional forms between different groups of
atoms, this can be set through energy groups. Different tables can be used
for non-bonded interactions between different energy groups pairs through
the .mdp option energygrp-table (see details in the User Guide). Atoms that
should interact with a different potential should be put into different
energy groups. Between group pairs which are not listed in energygrp-table,
the normal user tables will be used. This makes it easy to use a different
functional form between a few types of atoms.

Maybe you want to check out the whole section there. ;-)

Mark

On Tue, Mar 13, 2018 at 5:26 PM Debdas Dhabal <ddhabal at seas.upenn.edu>
wrote:

> Dear Mark,
>
> It would be very grateful if you could please comment on my confusion
> mentioned above.
>
> Thank you very much.
>
> With regards
> Debdas
>
>
>
> On Mon, Mar 12, 2018 at 4:20 PM, Debdas Dhabal <ddhabal at seas.upenn.edu>
> wrote:
>
> > Dear Mark,
> >
> > Thanks for your response. Yes, I have gone through that document. (link:
> > http://www.gromacs.org/@api/deki/files/94/=gromacs_nb.pdf).
> >
> > I have tried using energy-group pairs to take from table file and those
> > are not in the energygrps should take from Gromacs. But the document says
> > that the remaining interaction should be then calculated from default
> table
> > file named "table.xvg". Hence, in my case, if I only supply pair
> > interaction between *solute-solute* and* solute-solvent* (for which I
> > need to customize interaction) in *"table_solute_solute.xvg"* and default
> > "*table.xvg"* file respectively. Then Gromacs is taking *solvent-solvent*
> > interaction (for which I want to use the Gromacs normal thing and I
> haven't
> > given a table file) form that default *"table.xvg"* file. This means all
> > the remaining interaction (for which I haven't given the table file or
> > didn't mention in the energygrps)  is calculated using default
> "table.xvg"
> > file. But this not what I wanted. I want to take solvent-solvent
> > interaction from Gromacs defined LJ potential.
> >
> > At the bottom of the page no 6 of that document also says that
> > "It is important to note however that when a combination of Lennard Jones
> > and Buckingham terms is required tabulated potentials must be used for
> all
> > the non-bonded interactions even for the Lennard Jones."
> >
> > This means if I use *"vdwtype = User"* then I must have to supply all the
> > interaction using table file and cannot use both table and Gromacs
> defined
> > potential simultaneously ?. Kindly correct me if I got the meaning of
> that
> > line wrong.
> >
> > I will be waiting for your valuable comments. Thanks so much
> >
> > with regards
> > Debdas
> >
> > On Mon, Mar 12, 2018 at 12:33 PM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > wrote:
> >
> >> Hi,
> >>
> >> Yes, you can specify which energy-group pairs get which tables, and
> which
> >> do not get any (thus get the normal thing). Did you check out the
> >> documentation yet?
> >>
> >> Mark
> >>
> >> On Mon, Mar 12, 2018 at 5:30 PM Debdas Dhabal <ddhabal at seas.upenn.edu>
> >> wrote:
> >>
> >> > Hello everyone,
> >> >
> >> > Could anyone of you help me regarding the aforementioned problem. It
> >> would
> >> > be very nice of you.
> >> >
> >> > Thanks in advance.
> >> >
> >> > With regards
> >> > Debdas
> >> >
> >> > On Sat, Mar 10, 2018 at 1:30 PM, Debdas Dhabal <
> ddhabal at seas.upenn.edu>
> >> > wrote:
> >> >
> >> > > Dear Mark,
> >> > >
> >> > > Thanks  so much for your prompt reply. I had gone through that
> manual
> >> and
> >> > > I was able to use two different non-bonded potential for two
> different
> >> > > energy groups using table potential. But my question is a bit
> >> different.
> >> > > May be I was not able to make my question clear. I know the fact
> that
> >> by
> >> > > using table file I can use two different non bonded potential but
> >> what I
> >> > > wanted to ask whether it is possible to use table file only for user
> >> > > defined potential and not for which Gromacs already have predefined
> >> > > potential at the same time.
> >> > >
> >> > > Let me make it more clear. I have a system of solute in water. I
> want
> >> to
> >> > > use table file for only solute-water interaction and want to let the
> >> > > Gromacs take LJ potential for water-water interaction (ie. I don't
> >> want
> >> > to
> >> > > explicitly supply water-water interaction through Table file). In
> >> another
> >> > > way one can ask if I put *"vdwtype=User"* then is it *mandatory* to
> >> give
> >> > > non-bonded potential for both solute-water as well as water-water
> >> > > interaction through Table file only, or one can only use Table file
> >> for
> >> > > solute-water and Let the Gromacs take its predefined LJ potential
> form
> >> > for
> >> > > water-water interaction (as in case of vdwtype = Cut-Off case). So
> >> > > basically using Gromacs predefined potential and table potential at
> >> the
> >> > > same time.
> >> > >
> >> > > I hope I am able to make my question more clearer than before.
> Thanks
> >> > > again for your help.
> >> > >
> >> > > With regards
> >> > > Debdas
> >> > >
> >> > > On Sat, Mar 10, 2018 at 7:52 AM, Mark Abraham <
> >> mark.j.abraham at gmail.com>
> >> > > wrote:
> >> > >
> >> > >> Hi,
> >> > >>
> >> > >> Yes, if you check out the documentation of tabulated non-bonded
> >> > >> interactions in the reference manual, you will see that you can
> apply
> >> > >> different tables for particles when drawn from different energy
> >> groups.
> >> > >>
> >> > >> Mark
> >> > >>
> >> > >> On Sat, Mar 10, 2018 at 1:06 AM Debdas Dhabal <
> >> ddhabal at seas.upenn.edu>
> >> > >> wrote:
> >> > >>
> >> > >> > Hello everyone,
> >> > >> >
> >> > >> > This question may be very simple to most of the Gromacs user. I
> >> wonder
> >> > >> if
> >> > >> > Gromacs allow us to use both user-defined non-bonded potentials
> >> (Table
> >> > >> > potential) as well as Gromacs predefined potential at the same
> >> time.
> >> > For
> >> > >> > example, if I have a system with a solute in a solvent and for
> >> > >> > solvent-solvent nonbonded interaction, I want to use Gromacs
> >> defined
> >> > LJ
> >> > >> > potential but for solute-solvent nonbonded interaction, I want to
> >> use
> >> > a
> >> > >> > custom potential using a Table format. I know that
> solvent-solvent
> >> > >> > interaction can also be incorporated in the Table file and we can
> >> run
> >> > >> > Gromacs successfully, but I want to use Table potential only for
> >> which
> >> > >> > Gromacs does not have predefined form.   Is it possible ?. If
> so, I
> >> > >> would
> >> > >> > be grateful if someone could suggest me to how to do that?.
> >> > >> >
> >> > >> > I will appreciate all your valuable inputs. Thanks so much in
> >> advance.
> >> > >> >
> >> > >> > --
> >> > >> > Debdas Dhabal
> >> > >> > Postdoctoral Researcher.
> >> > >> > SEAS, Department of Chemical and Biomolecular Engineering,
> >> > >> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >> > >> > --
> >> > >> > Gromacs Users mailing list
> >> > >> >
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> before
> >> > >> > posting!
> >> > >> >
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> >> > >> > send a mail to gmx-users-request at gromacs.org.
> >> > >> >
> >> > >> --
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> >> > >>
> >> > >
> >> > >
> >> > >
> >> > > --
> >> > > Debdas Dhabal
> >> > > Postdoctoral Researcher.
> >> > > SEAS, Department of Chemical and Biomolecular Engineering,
> >> > > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >> > >
> >> >
> >> >
> >> >
> >> > --
> >> > Debdas Dhabal
> >> > Postdoctoral Researcher.
> >> > SEAS, Department of Chemical and Biomolecular Engineering,
> >> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >> > --
> >> > Gromacs Users mailing list
> >> >
> >> > * Please search the archive at
> >> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> > posting!
> >> >
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> >> >
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> >> > 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!
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> >>
> >
> >
> >
> > --
> > Debdas Dhabal
> > Postdoctoral Researcher.
> > SEAS, Department of Chemical and Biomolecular Engineering,
> > The University of Pennsylvania, Philadelphia, PA 19104, USA.
> >
>
>
>
> --
> Debdas Dhabal
> Postdoctoral Researcher.
> SEAS, Department of Chemical and Biomolecular Engineering,
> The University of Pennsylvania, Philadelphia, PA 19104, USA.
> --
> Gromacs Users mailing list
>
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