[gmx-users] Membrane-protein tutorial

[mohsen ramezanpour]

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.

Am I right?
thanks in advance
mohsen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110307/6712a5e0/attachment.html>