Juliette N. wrote:
On 24 February 2012 16:52, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Juliette N. wrote:
On 23 February 2012 21:18, Mark Abraham <[email protected]
<mailto:[email protected]>
<mailto:[email protected].__au
<mailto:[email protected]>>> wrote:
On 24/02/12, *"Juliette N." *<[email protected]
<mailto:[email protected]>
<mailto:[email protected]
<mailto:[email protected]>>__> wrote:
On 23 February 2012 20:07, Mark Abraham
<[email protected] <mailto:[email protected]>
<mailto:[email protected].__au
<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.
Thank you Justin.
1- The input values to g_sigeps has to be the geometric mean of two
materials then?
I think g_sigeps is designed to produce simple plots for single atom types, but
I suppose you can tweak it. If you're looking for a simple difference in energy
based on distance, you can do that in a few moments with a calculator and the
Lennard-Jones equation.
I have also another trivial question. The OPLS 1984 paper, Optimized
Intermolecular Potential Functions for Liquid
Hydrocarbons states:
The cutoff distance for the intermolecular interactions was a little
less than half the average length of an edge of the periodic
cube. It ranged from 9.5 A, for methane to 13 A, for benzene and 15 A,
for n-hexane.
My enquiry is that,
2-is this cutoff mentioned above the parametrization cutoff or the
cutoff that has only been used in that paper?
Hence the problem with using OPLS, in some cases. That paper was probably for
the old OPLS-UA parameters (which are part of Gromacs, but are outdated) and
exemplifies how each system differed in terms of cutoffs.
3- If thats the cutoff that was used in parametrization, since atom
types of hexane, propane, heptane, ....and even saturated polymers
C-C-C-C........C are identical in atp file, does this mean for all
alkanes and such polymers rc =15 A must be used?
Again it depends on the nuts and bolts of the simulation. The paper you cite is
quite old and thus more modern algorithms for electrostatics, energy
conservation, etc were not available. I'd do some digging into more recent
literature from people who have done similar things to see what they recommend.
For proteins, rc=rvdw=rlist=1.0 works well in conjunction with PME for
electrostatics.
-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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