Some question about only using single tabular potential in gromacs

[Ran Zhao]

Hello, I am preparing to simulate the polymer in a water solution using the Martini force field.

In the simulation model, I want to set a specific tabular potential between water beads. And other beads still follow the martini force field.

In gromacs, when one wants to use tabular potential, some lines should be added in .mdp file:

vdwtype                    = User

rvdw                          = 1.0

energygrps               = POL (the name of type of water bead)

energygrp_table       = POL POL

the mdrun command will read the table_POL_POL.xvg

But, I want mdrun to read the force field of other beads from the martini .itp file.

Is it possible for me to do this in gromacs?

Looking forward to and thank you for your answer

Sincerely yours

                    Ran

[Christoph Junghans]

On Sun, Apr 9, 2023 at 9:01 AM Ran Zhao <ranzh...@gmail.com> wrote:
>
> Hello, I am preparing to simulate the polymer in a water solution using the Martini force field.
> In the simulation model, I want to set a specific tabular potential between water beads. And other beads still follow the martini force field.
>
> In gromacs, when one wants to use tabular potential, some lines should be added in .mdp file:
> vdwtype = User
> rvdw = 1.0
> energygrps = POL (the name of type of water bead)
> energygrp_table = POL POL
> the mdrun command will read the table_POL_POL.xvg
> But, I want mdrun to read the force field of other beads from the martini .itp file.
> Is it possible for me to do this in gromacs?

I think this is more a question for the gromacs mailing list, but as
far as I know you cannot mix tabulated with non-tabulated
interactions.
You can still make that work as Gromacs will read a standard LJ 6-12
table (table.xvg) for all groups that aren't covered by the pairs in
energygrp_table though.

Christoph

> Looking forward to and thank you for your answer
>
> Sincerely yours
> Ran
>

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--
Christoph Junghans
Web: http://www.compphys.de

[Ran Zhao]

Thank you for the helpful reply.

From my point of view, I need to create some tabular potentials for other pairs of beads according to the \epsilon and \sigma of standard LJ 6-12 potential existing in the martini .itp file.

After doing this thing, I can run my simulation.

Sincerely yours
                    Ran