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

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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