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

[Mark Abraham]

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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> >
> >
> >
> > --
> > 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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