[gmx-users] suitable parameter settings for intermolecular non-bonded interaction

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 31 13:39:36 CEST 2010

On 31/03/2010 9:15 PM, vedat durmaz wrote:
> hello out there,
> i'm trying to simulate a receptor ligand system in order to extract
> intermolecular non-bonded interaction energies (vdw/coulomb) and apply
> the linear interaction energy model.

Agreed on Sander's point, here.

> which parameter settings do you recommend for highly accurate results?
> up to now, i had chosen (copied from somewhere :)

Well, write it down, because you'll need to defend your choices later :-)

> rlist                = 1.2
> vdwtype              = shift
> rvdw                 = 1.0
> rvdw-switch          = 0.9
> coulombtype          = PME-Switch ; PME
> rcoulomb             = 1.1
> resulting in LJ-14 = 0, and Coulomb-14 = 0 (which i "intuitionally"
> prefer to LJ-SR and Coulomb-SR).

I've no idea what you mean by this.

> i have a box of 8.1857 x 8.1857 x 8.1857 nm. Is it helpful to increase
> rcoulomb and rvdw up to e.g. 8.0 and rvdw-switch up to 4.0 or/and should
> i take vdwtype=cut-off instead of shift?? what's the difference? how can
> i get my LJ-14/Coulomb-14 terms? can anyone provide a well-working
> combination of parameter settings for non-bonded interactions within a
> system as described above?

As I wrote earlier today, haphazardly varying parameters is not what you 
want to do. Merely increasing these cut-offs may feel like "more 
accuracy", but computing a more expensive approximation to a theoretical 
model is not necessarily any good, because the parameters you are using 
were developed for some different cut-off. It does not follow that the 
parameters are transferable to other contexts. You should aim to use a 
model physics for which the parameters were developed, or for which they 
were subsequently proved to be effective.

> that's quite a lot questions, i know.
> gromacs says: "Refer to the primary literature for your of choice for
> the recommended settings". However, i couldn't find any recommondations
> for ffamber99 (ffamber99sb is what i use) in the pdf documents provided
> with the amber port's download.

They're not primary literature. Refereed publications tend to accompany 
the introduction of forcefields, and they are mandatory reading. AMBER 
(port)'s webpage will tell you what to read. Also search for subsequent 
work by the same authors, for they are probably using best practice for 
their own forcefield...


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