Thermodynamic Integration (free energy of conformation change)

From: Kramer Campen (
Date: Mon Jan 08 2007 - 12:11:02 CST

Hey Folks:

I have a quick question about the standard MCTI block (as written in the
NAMD user's guide) that I thought others might be able to answer...

A section of the MCTI input might look like....

mcti {
   task = stepup
   equiltime = 10 ps
   accumtime = 10 ps
   numsteps = 36
   print = 1 ps

In this arrangement the free energy will be printed 10 times at each value
of lambda (at ps 1, 2, 3, etc...). My question is whether the value of
free energy printed at ps 2 is based on the simulation data from 1-2 ps or
from 0-2 ps?

I suspect it makes sense to average over the entire length of the accumtime
but the documentation is a bit scanty on this point.

Thanks in advance for any insight.

Kramer Campen

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