[gmx-users] Using lennard jones and buckingham terms simultaneously

Gareth Tribello gareth.tribello at gmail.com
Thu Mar 25 21:03:13 CET 2010

Hello again

I have tried to do as you suggest and use tables but I have a new problem.
 First let me describe my process and then you can let me know if there is
anything wrong in the stages:

OK so first you include the following directives into the mdp file:

coulombtype = pme   (or whatever sort of coulomb interaction you are using)
vdw-type = user

energygrps          = Ca CCA OCA OW HW
energygrp_table   = Ca OCA Ca CCA OCA OCA OCA OW OCA HW

Gromacs is then (at some stage) going to look for a series of files called

table.xvg  -   which is the default 6-12 Lennard Jones that will be used for
most of the atoms
table_Ca_OCA.xvg  - which are the Buckingham interactions between your
various atom types.

These files have the format (and contents) described in section 6.7 of the
manual.  Finally, you define the various energy groups Ca, OCA and so on in
your index.ndx file.

The problem is that grompp gives me the following error:

"atoms 1 and 2 in charge group 1 of molecule type 'SOL' are in different
energy groups"

(incidentally these atoms 1 and 2 are OW and HW)

Does this mean that I cannot use different tabulated potentials for
different atoms in a molecules?  By which I mean that I can't use different
tabulated potentials for the OW Ca and HW Ca interactions for example?

Final question, as its not clear to me from the manual, if you use a
tabulated potential for Lennard Jones and you use mix type 2 (so are you are
providing epsilon and sigma in the input rather than A and B) does gromacs
still know that it has to manipulate the input parameters in order to get
the coefficients of the (tabulated) g(r) and h(r) dispersion and repulsion
functions (I mean the g(r) and h(r) defined in section 6.7 of the manual
here)?  At the same time does it also know not to do anything to the
parameters you input for the (tabulated) buckingham potentials (as for a
buckingham you are providing A and C)?

Many thanks in advance

On Wed, Mar 24, 2010 at 2:25 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

> ----- Original Message -----
> From: Matthew Watkins <matthew.watkins at ucl.ac.uk>
> Date: Wednesday, March 24, 2010 2:59
> Subject: Re: [gmx-users] Using lennard jones and buckingham terms
> simultaneously
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Hi Gareth,
> >
> > as Vitaly suggested tabulated potentials seem to be the only way
> > to go, it took me a while to get up to speed on the Gromacs way
> > of doing this, so get in touch if you wish.
> >
> > The tables for buck potentials need to include the standard 1/r6
> > term whilst what would be the 1/r12 term needs to contain exp(-
> > Bx.rho), the C6 and C12 coefficients can then be put in a
> > standard nonbonded section.  You'll need a separated table
> > for each pair of interactions that interact with buckingham
> > potential.  Each pair must be an energy group as well.
> >
> > If there is a simpler method I'd love to hear it.
> There's probably not a simpler method because it's not a widely-used
> procedure. It shouldn't be used at all unless you have established that the
> combination of functional forms is effective...
> Mark
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