[gmx-users] About Physaica Parameter
jalemkul at vt.edu
Tue Jun 4 13:38:25 CEST 2013
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
> 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
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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