[gmx-users] About Physaica Parameter

[Justin Lemkul]

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

-- 
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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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