[gmx-users] Membrane-protein tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Mar 7 16:45:10 CET 2011

mohsen ramezanpour wrote:
> Dear Dr.Justin
> Is there any criteria for choosing vdwradii for carbon atoms?
> Because I have changed it from 0.15 to 0.375,but there were afew water 
> molecules,it is difficult to delete them manually.
> then I decided to increase the vdwradii to 0.450
> it is better now but i think the gap between water surface and lipids 
> surface is a little big,although there are still  a few water molecules 
> between lipids.
> But this work can reduce the interactions between water molecules and my 
> system in the next steps.

There is no scientific way to choose a new vdW radius.  Your problem indicates 
that you probably haven't achieved sufficient packing of your lipids.  I can't 
think of a time when a vdW radius for carbon > 0.375 was necessary for a 
properly-packed system.  You can also write a script to remove waters within a 
certain range of z-coordinates, and in fact, there is one on the Gromacs website 
that might be useful.  If you have to remove lots of water, it indicates that 
your lipids aren't sufficiently packed and equilibration will take a lot longer 
than it should.


> Am I right?
> thanks in advance
> mohsen 


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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