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

vedat durmaz durmaz at zib.de
Wed Mar 31 12:15:21 CEST 2010

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


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