Marcelo Silva wrote:
Hi,
I am trying to simulate mixtures of ethanol and trifluoroethanol and I
would like to use the same parameters used on OPLS parametrization.
On the OPLS1996 paper the authors starts by stating that they've used
267 molecules and "The box size varied from approximately 26 26 26 Å
for methanol to 37 37 37 Å for cyclohexane". In my simulations I am
considering using 500 molecules (each box vector would be around 37 Å).
"In most cases, the intermolecular nonbonded interactions were truncated
at 11Å based on roughly the center-of-mass separations with quadratic
smoothing of the interaction energy to zero over the last 0.5 Å (...) A
standard correction was made for the Lennard-Jones interactions
neglected beyond the cutoff."
Trying to interpret what is written I think the correct way to treat
cut-offs and energy corrections would be like this:
---------------------------------------
Cut-offs
rlist = 1.4
coulombtype = Reaction-field-zero
rcoulomb = 1.1
rcuolomb_shift = 0.6
vdwtype = shift
rvdw = 1.1
rvdw_switch = 0.6
Dispersion Correction
DispCorr = EnerPress
---------------------------------------
However I have some doubts because I'm using a box with a different
number of molecules/ different size (should I change the cutoffs to 15Å
like it was for cyclohexane?) and I'm not sure about using
Reaction-field-zero instead of the shift function for coulombic
interactions.
Could you please help me confirm this parameters so I can run a
simulation in the same conditions as OPLS was parameterized (although
using MC and not MD).
I don't think there is a perfectly clear answer to this. OPLS was initially
designed for MC with some special functional forms and is now applied to MD
using all manner of settings. Commonly, one sees rcoulomb=rvdw=rlist=1.0 or 1.4
in conjunction with PME. There have been a variety of systematic force field
comparisons in recent years. You should consult those to see what their
specific recommendations are with respect to proper settings, although many of
them focus on proteins.
-Justin
Best regards,
Marcelo
--
========================================
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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