[gmx-users] Re: Tabulated potentials and normal nonbonded interaction at the same time

Thomas Schlesier schlesi at uni-mainz.de
Thu Sep 16 11:48:36 CEST 2010

first, thank you for you're answers.
I looked more into the stuff.

I think i would use the following setup:

Since the CG-solvent is uncharged, i can use the normal 
coulomb-interaction (PME) for the system.

For the vdw-part, i would use 'vdw_type=user' and:
energy_grps = CG Mol
energygrp_tables = CG CG (CG self-interaction) CG Mol (CG-Molecule 
(CG = CG-solvent; Mol=Molecule)
So i would need two tables (for each interaction one).
With this i should get all the vdw-interaction where the CG-solvent is 

But since i need normal vdw-interactions for the Molecule 
self-interaction, i would need in the .mdp-file
'vdw_type = user' AND 'vdw_type = cut-off'

Or am i wrong (hope so)? Because the only way i can think of to solve 
the problem, would be that i make for every vdw-self-interaction of the 
Molecule an own table, which wouldn't be good (since i read somewhere 
that tables are slower then to calculated the interaction normally).

So how could i solve the problem, or this there no problem because i 
didn't understand the whole stuff correctly (seems so because of Marks 


 >> Hello
 >> >
 >> > I think what you need to do is use multiple tables.  So you
 >> > have one
 >> > table for your CG-solvent interaction with itself and then
 >> > another one
 >> > for your CG-solvent (uncharged) interactions.  (This second table
 >> > would then just a tabulated version of the Lennard Jones >interaction
 >> > or whatever you are using.)   This page might be of help:
 >> >
 >> > http://www.gromacs.org/Documentation/How-tos/Tabulated_Potentials
 >While this would work, the key piece of information is that GROMACS 
 >will permit you to use different tables only for selected 
 >inter-energy-group interactions. So the OP needs suitable energy 
 >groups, and only one table. The other groups use the normal >interactions.
 > >
 > > ciao
 > > Gareth
 > >
 > > On Wed, Sep 15, 2010 at 5:40 PM, Thomas Schlesier
 > > <schlesi at uni-mainz.de> wrote:
 >> > > Dear Gromacs-User,
 >> > > i want to try to simulate an atomistic molecule with CG-
 > > solvent (uncharged).
 >> > > For the atomistic molecule i want to use the normal non-bonded
 > > interactions,> but for the CG-solvent interaction with itself
 > > and the molecule i need a
 >> > > tabulated potential.
 >> > > So my question is, is that possible to do in Gromacs?
 >> > > I looked a little bit into the manual and it seems that
 > > tabulated potentials
 >> > > use the 'vdw_type' and/or the 'coulomb_type' keyword, which i
 > > will need for
 >> > > the normal interactions.
 >> > > Greetings
 >> > > Thomas
 >> > > --
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