Problems about FEP simulation

From: Yang Gao (
Date: Fri May 21 2010 - 11:03:08 CDT

Dear All,

I am Yang Gao, from Iowa State University. Recently, I am conducting some
FEP simulation to calculate water energy in a big cavity. The dimension of
the cavity is somewhat big, ~12 by 20 by 24 A. In the simulation setup, each
water is gradually replaced with a DUMMY atom. The problem is whenever I did
minimization for the FEP system, I will get the "bad global exclusion count"
error. I have checked the psf file and seems the exclusion list in it is
good. Later I noticed this problem could be that my water are far away from
each other (could be as far as 24 A). So I enlarge the cutoff to 24, and the
error disappeared.

So my question here is: First, could this cutoff be the reason for the "bad
global exclusion count" error? If so, is there any other way to solve this
problem other than bigger cutoff? And then will this big cutoff be a big
problem besides making the simulation slow?

I really appreciate any help or suggestions. Thank you very much.


This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:54:09 CST