Free Energy of Conformational Change PMF - documentation on method?

From: David Sivak (sivak_at_berkeley.edu)
Date: Thu Mar 13 2008 - 18:07:56 CDT

Hi, relative NAMD-newbie here, forgive me if I'm overlooking anything
obvious. I'm looking for any further documentation for the Free Energy of
Conformational Change module's calculation of delta G. I'm currently using
PMF, but I'd also like to know about MCTI for future reference. In
particular, I can't find the specifics on how the delta-G column in the
output (see sample FreeEnergy output below) is calculated from the
simulation, either in the User's Guide or Tutorials or Mailing List. There
have been some unanswered questions to NAMD-L about this topic by others in
the past, but hopefully this time around there's somebody out there that can
point me in the right direction. Many thanks in advance.

David

Here is a sample of the FreeEnergy output, where these are the first few
lines grep'ped from the output log file:

FreeEnergy: nstep time(ps) task lambdaKf lambdaRef delta-G
#steps n*{value target |}
FreeEnergy: ----- -------- -------- -------- --------- ----------
------ -------------------
FreeEnergy: 5 0.010 Up 1.00000 0.00001 -6.60e-01
5 179.768 179.998 |
FreeEnergy: 10 0.020 Up 1.00000 0.00002 -1.26e+00
10 178.528 179.996 |
FreeEnergy: 15 0.030 Up 1.00000 0.00003 -1.63e+00
15 179.757 179.995 |
FreeEnergy: 20 0.040 Up 1.00000 0.00004 -2.20e+00
20 178.838 179.993 |
FreeEnergy: 25 0.050 Up 1.00000 0.00005 -2.47e+00
25 179.482 179.991 |
FreeEnergy: 30 0.060 Up 1.00000 0.00006 -2.97e+00
30 179.174 179.989 |
FreeEnergy: 35 0.070 Up 1.00000 0.00007 -3.19e+00
35 179.324 179.987 |
FreeEnergy: 40 0.080 Up 1.00000 0.00008 -3.62e+00
40 179.461 179.986 |

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