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.
-Justin
Am I right?
thanks in advance
mohsen
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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