Hi Mark!
I think that this is the paper that you are referring to:
dx.doi.org/10.1021/ct900549r
Also for your reference, these are the settings that Justin recommended
using with CHARMM in gromacs:
vdwtype = switch
rlist = 1.2
rlistlong = 1.4
rvdw = 1.2
rvdw-switch = 1.0
rcoulomb = 1.2
As you mention the switch function in gromacs is different than in CHARMM
but it appears that the difference is very small.
Gianluca
On Thu, 7 Nov 2013, Mark Abraham wrote:
Reasonable, but CPU-only is not 100% conforming either; IIRC the CHARMM
switch differs from the GROMACS switch (Justin linked a paper here with the
CHARMM switch description a month or so back, but I don't have that link to
hand).
Mark
On Thu, Nov 7, 2013 at 8:45 PM, rajat desikan <rajatdesi...@gmail.com>wrote:
Thank you, Mark. I think that running it on CPUs is a safer choice at
present.
On Thu, Nov 7, 2013 at 9:41 PM, Mark Abraham <mark.j.abra...@gmail.com
wrote:
Hi,
It's not easy to be explicit. CHARMM wasn't parameterized with PME, so
the
original paper's coulomb settings can be taken with a grain of salt for
use
with PME - others' success in practice should be a guideline here. The
good
news is that the default GROMACS PME settings are pretty good for at
least
some problems (http://pubs.acs.org/doi/abs/10.1021/ct4005068), and the
GPU
auto-tuning of parameters in 4.6 is designed to preserve the right sorts
of
things.
LJ is harder because it would make good sense to preserve the way CHARMM
did it, but IIRC you can't use something equivalent to the CHARMM LJ
shift
with the Verlet kernels, either natively or with a table. We hope to fix
that in 5.0, but code is not written yet. I would probably use vdwtype =
cut-off, vdw-modifier = potential-shift-verlet and
rcoulomb=rlist=rvdw=1.2,
but I don't run CHARMM simulations for a living ;-)
Mark
On Thu, Nov 7, 2013 at 1:42 PM, Rajat Desikan <rajatdesi...@gmail.com
wrote:
Dear All,
Any suggestions?
Thank you.
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Prof. K. Ganapathy Ayappa's Lab (no 13),
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Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
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Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
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