On 6/4/13 5:06 AM, vidhya sankar wrote:
Dear Justin & Mark Thank you for your previous reply
I
am doing Simulation of CNT wrapped By Cyclic Peptide in Water For that I have
used the Parameters as follows for my production run
ns_type = grid
nstlist = 5
rlist = 1.8
rcoulomb = 1.2
vdwtype = Shift
rvdw = 1.2
coulombtype = Reaction-Field-zero
pme_order = 4
fourierspacing = 0.16
pcoupl = Parrinello-Rahman
pcoupltype = semiisotropic (Because My system is Composed of both pure
Hydrophobic(CNT) & Hydrophilic IProtein) part and Immersed in water)
tau_p = 2.0
ref_p = 1.0 1.0
compressibility = 4.5e-5 4.5e-5
It run well
But How to check is all these parameters are wright or wrong?
Is Theer is Any thumb rule to Assign parameters ?
The cutoffs look bizarre. They should be set based on the parent force field.
Because My system is Composed of both pure Hydrophobic(CNT) & Hydrophilic
IProtein) part and Immersed in water so I have Selected semiisotropic
That does not make sense. Semiisotropic coupling is for systems that deform in
x-y and z independently, not due to the chemical nature of the molecules in the
system.
What are the parameters Should i Concentrate and How to choose its value carefully
& rationally ?
Base your settings on a thorough understanding of your chosen force field and an
examination of the literature for other algorithms to understand their benefits
and limitations.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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