On Sep 9, 2009, at 6:01 PM, Li Yang wrote:
Dear GMXers:
I'm sorry to disturb you.
I have a question about the Marrink's coarse-grained model, Marrink,
et al. Coarse Grained Model for Semiquantitative Lipid Simulations.
J. Phys. Chem. B 2004, 108, 750-760.
First of all you should upgrade your model to the new version of this
model (the MARTINI CG model).
Marrink et al JPC/B 2007, 111, 7812-24
Monticelli et al JCTC 2008, 4, 819-34
In the Marrink's CG model, the electrostatic Coulombic potential is
computed via cutoff scheme. In the original paper, the cutoff method
is employed "with relative dielectric constant \epsilon=20 for
explicit screening". Does it mean the parameter of force field is
only customized for the cutoff method? As known that the Ewald
method is better than the cutoff scheme for the long-range
electrostatic interaction. I want to know whether the Ewald method
is also OK for this model? How can I test it? I have simulated a
similar system via two method respectively, which includes a big
charged nano-scale particle (~6nm). But I find that the results of
cutoff scheme are quite different from the PME's results. I don't
know which one is right.
The model per se is parameterized using epsilon=15 (new version) and
a cutoff scheme.
This is what people should use, as if you change it you will alter the
thermodynamics
properties of the model and thereby modify it.
Then some test have been made with PME for the electrostatic for
bilayer systems.
Although some phenomenon does not appear in the same time scale the
overall
properties of a bilayer are not affected significantly. If you choose
to use PME
with MARTINI, you should make some test on your specific system to see
whether
it affects the behavior of the model.
Note that PME is good at some things a cutoff scheme is bad but it
introduces others
(effect of periodicity on small system, increased computational
cost ...).
You should find some literature on this.
XAvier.
Another question is how to get the relative dielectric constant for
a CG model. I'm not familiar with this topic, but I think it is the
key of the above question perhaps. Yet, there are not some details
in the original paper. In some other paper about different CG
models, I don't find some information about this topic. Could
someone please give me some refs about the computational details?
Thank you very much.
Li Yang
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