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

[Debdas Dhabal]

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.
> > >> > --
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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.
> > --
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-- 
Debdas Dhabal
Postdoctoral Researcher.
SEAS, Department of Chemical and Biomolecular Engineering,
The University of Pennsylvania, Philadelphia, PA 19104, USA.