Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 24/02/12, *"Juliette N." *<[email protected]
<mailto:[email protected]>> wrote:
On 23 February 2012 20:07, Mark Abraham <[email protected]
<mailto:[email protected]>> wrote:
On 24/02/2012 10:55 AM, Juliette N. wrote:
Hi all,
My average size is 2.9 nm obtained from NPT under large
pressure and now I intend to increase rc to 1.4 and rlist to
1.65 nm. I am just worried about violating minimum image
convention.
That probably violates the parametrization of your force field.
Thanks Mark. You mean rc =1.4 for OPLS-AA is not appropriate? In
the original OPLSAA: Optimized Intermolecular Potential
Functions for Liquid Hydrocarbons
I see rc of 15 A has been used for alkanes which requires rlist of
around 15+2.5+17.5 A ! Please comment why I am violating
parametrization? Thanks.
It is appropriate to use a set of .mdp parameters that most closely
reproduce the parametrization conditions, or other conditions that
have been shown to be effective. So if you were using rc<1.4 and now
want to use rc=1.4, then it is likely that at least one of those
choices is inappropriate. If 1.5nm was used in parameterization,
then both the foregoing are probably unsuitable. The values for
other rxxx parameters should be addressed in that work, and will
depend on charge group size and electrostatics model.
Thank you Mark. I was using rc =1.1 and just wanted to how much my
results vary by applying rc of 1.4 nm. I dont know the exact value that
was used in parametrization. I have just seen some previous works with
cut offs around these values. Is there anyway I can obtain plot of LJ
potential versus distance?
For any sigma and epsilon values, you can obtain such a plot with g_sigeps.
The problem with the original OPLS parameterization was that different cutoffs
were used for different types of molecules. Shifted potentials were used
instead of PME, which can change the way electrostatics are handled if using the
latter method. Probably someone, somewhere along the way, has published
recommendations for normal use in whatever type of system you're dealing with.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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