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

Tue Mar 13 19:07:00 CET 2018

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On Tue, Mar 13, 2018 at 1:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> 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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> > >> > >> > posting!
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> > >> > >> >
> > >> > >> --
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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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> > >
> > >
> > >
> > > --
> > > 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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> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
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