On 31/03/2010 11:44 PM, vedat durmaz wrote:
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.
Sure... it's still only an algorithm that generates a fairly coarse
approximation.
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),
Well that means they weren't calculated. Whether that's reasonable
depends on your forcefield.
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?
*Tend*? Your usage of that word makes no scientific sense that I can
see. What on earth is more significant about non-bonded interactions
between atoms separated by 3 bonds than other non-bonded interactions? :-)
Mark
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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
