[gmx-users] Value of atom C in vdwradii.dat _ Protein-membrane system

[Justin Lemkul]

On 10/1/12 8:23 AM, Shima Arasteh wrote:
> Dear gmx users,
>
> I want to simulate a system of lipid-protein. I am following the protocol of Justin's KALP-15 tutorial.
> After packing lipids around protein, I need to run genbox command. Before that, I copied vdwradii.dat. In KALP15-DPPC tutorial, it's suggested to change the value of C from 0.15 to 0.375. I want to know how did you choose 0.375 for value of C? Am I supposed to use this value in any other lipid-membrane system?
>

That value was based on trial and error.  Modify as necessary to achieve 
reasonable results.  It may not work universally.

-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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