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

[Debdas Dhabal]

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
>> > >> >
>> > >> > * 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.
>> > >>
>> > >
>> > >
>> > >
>> > > --
>> > > 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!
>> >
>> > * 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.
>>
>
>
>
> --
> 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.