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

vedat durmaz durmaz at zib.de
Wed Mar 31 14:44:11 CEST 2010

thanks to both of you for your helpful hints. actually, i'm not using
the LIE method as available with the gromacs package, but planning to
implement the model myself using energies from gromacs runs.

be that as it may, one thing remained unclear (see below please).

 Mark Abraham schrieb:
> 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.

what i mean is that after having applied "g_energy" to the energy output
file in order to extract non-bonded energies, all "Coulomb-14" and
"LJ-14" terms shape up to be equal to zero (as if they haven't been
calculated), but "Coulomb-SR" and "LJ-SR" are plausible decimal numbers
like for example -48.1234. though, at the moment i "tend" to operate on
*-14 energies. how can i tell gromacs to compute these terms?

>> 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...
> Mark

More information about the gromacs.org_gmx-users mailing list