Em 02-04-2011 0:33, Justin A. Lemkul escreveu:
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
Just to test it, I used this options (nstlist = 5 with timestep 1fs):
; Cut-offs
rlist = 1.4
coulombtype = Switch
rcoulomb = 1.1
rcuolomb_shift = 1.05
vdwtype = Switch
rvdw = 1.1
rvdw_switch = 1.05
; Dispersion Correction
DispCorr = EnerPres
and compared to vdw plain cutoff at 1.1 and PME with cutoff 1.1 nm
(rlist = 1.1 nm also). The big difference in the output seems to be with
the Coulomb (SR) term:
-1.25490e+05 kj/mol with Switch
-5.38895e+03 kj/mol with PME
With switch I get a low density for ethanol (about 0.3 g/ml). What could
be the problem with the simulation using switch? By the way does gromacs
use a different switch function depending on the forcefield?
Best regards,
Marcelo
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