[gmx-users] vdwd option on genbox: Exactly what does it do?

David Mobley dmobley at gmail.com
Mon Jan 9 19:39:45 CET 2006

Dear all,

genbox has a -vdwd option which specifies "default vdwaals distance". The
documentation isn't too clear about this; does it override what genbox
usually uses? Or is it only used for molecules which have no vdW parameters
or some such?

For anyone who cares: I'm trying to keep water somewhat further away from
the protein when solvating than is typical, and I'm trying to figure out
whether using -vdwd is a way to do this, or whether I'll have to make a
script to delete all of the waters within my desired cutoff distance from
the protein.

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