AMBER Archive (2004)

Subject: AMBER: replica exchange with thermodynamic integration

From: david.evans_at_ulsop.ac.uk
Date: Thu Sep 23 2004 - 06:18:44 CDT

Dear list,

I'm curious about the option to use MMTSB in combination with lambda
replica-exchange (pg 150 Amber8 manual). I have a copy of the MMTSB
toolkit, but cannot find documented anywhere exactly what this option
does e.g.what is the acceptance probability used for exchange moves
between replicas with different lambda values. (My vague plan is to
run TI calculations at different lambda values in parallel, and use a
free energy perturbation-style exchange move to hopefully enhance
sampling.)

Could anyone with experience of using this tool explain this in more
detail, or give a reference?

Thanks

Dave Evans
London School of Pharmacy
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