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

Sander Pronk pronk at cbr.su.se
Wed Mar 31 12:56:45 CEST 2010

Hi Vedat,

If I understand it correctly, you're trying to calculate the free energy of binding using the LIE method. Then keep in mind that LIE is an approximate method, and that any accuracy you're trying to achieve is going to be limited by the approximations of LIE. 

Your 'primary literature' would in your case be the existing literature about LIE (e.g. Aqvist & Marelius, Comb Chem High Throughput Screen. 2001 Dec;4(8):613-26 and later publications). Those publications should address all of your issues, including the force fields to choose, and the vdw cut-off. 

One exception is the coulomb cut-off radius, which, used together with the fourier spacing, should be used to tune the amount of CPU time spent calculating real-space vs. reciprocal space calculations, and not so much the accuracy of the resulting energies.


On 31 Mar 2010, at 12:15 , 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.

> which parameter settings do you recommend for highly accurate results?
> up to now, i had chosen (copied from somewhere :)
> 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 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?
> 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.
> thanks a lot in anticipation
> vedat
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