AMBER Archive (2007)

Subject: AMBER: Addendum: Heat capacity calculations not coming out right

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Fri Oct 19 2007 - 22:31:46 CDT

I wanted to add that I was not at first taking into account the -2.22
cal/mol-K correction for quantum effects that Yujiw Wu did. This means
that ONE of my answers is closer to the value he reported, enough that I
would be satisfied with the agreement. I'm now repeating his experiment
as best I can in AMBER, but I have to use 256 molecules rather than 216
for fear that the box will get too tight for the 9A cutoff.

Out of curiosity, what would happen if the nonbonded pair list cutoff (as
opposed to the direct interaction cutoff) were larger than half the box
length?

Thanks!

Dave
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