> I can see a sort of cross-like empty shape between the
> 4 boxes that are added to solvate the entire protein, with the protein in
> the center
Leap is using vdw boundaries to place the boxes - it is safer than
assuming that the boxes themselves are periodic and thus intermesh
at the boundaries. Since the place-and-subtract algorithm also
creates voids around the protein itself, and solvent boxes are cut
at the edge of the overall solvation box and hence need to use net
vdw separation (i.e. can't intermesh), the inter-box voids are just
another source of the vacuum that needs to be equilibrated by NPT.
Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 25 2010 - 10:30:06 PDT
