VMD-L Mailing List

From: Papan S (spapan2012_at_gmail.com)
Date: Wed Apr 04 2012 - 08:16:00 CDT

Dear all,

For calculation of transport coefficients (unlike say, the RDF), it is
advisable to not adapt the minimum image convention while calculating
differences in position. However, say, one is interested in transport
properties of water on a biomolecular surface (say a protein). Since the
water on the surface will diffuse out, should not one wrap up the
simulation trajectories (ie. use min. image) to calculate transport
properties? Some advice is very much appreciated...

Thank you.
-PapanS