[gmx-users] Value of atom C in vdwradii.dat _ Protein-membrane system
jalemkul at vt.edu
Mon Oct 1 14:53:22 CEST 2012
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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