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...
Mark
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