From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Fri Jan 30 2015 - 14:15:01 CST
As a follow up, I think I've answered my own question. It appears that the
LJcorrection is "incorrectly" computed as the simple average of LJ types.
However, this should be a lambda weighted average. If not, the single
topology energy for lambda = 0 will not match the dual topology energy for
lambda = 0 unless the correction is turned off.
I've attached an exaggerated example for a simple ion system.
Eve in that test, the energy is small, but even for a simple peptide with a
hybrid sidechain, this disrepancy is ~0.3 kcal/mol. That's pretty serious
compared to expected statistical errors.
On Fri, Jan 30, 2015 at 12:10 PM, Brian Radak <brian.radak.accts_at_gmail.com>
> Could anyone tell me exactly how the LJcorrection works when alchemy is
> turned on? I'm trying to develop a simple test case, but it looks like the
> correction term is just quietly turned off when alchemy is turned on.
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail: radak_at_uchicago.edu
-- Brian Radak Postdoctoral Scholar University of Chicago Department of Biochemistry & Molecular Biology Gordon Center for Integrative Science, W323A 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 e-mail: radak_at_uchicago.edu
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