# [AMBER] MBAR calculation

From: Liu Denis <cndenis.gmail.com>
Date: Thu, 16 Aug 2012 23:33:21 +0800

Dear Amber members,

I am trying to calculation the free energy using mbar data in TI running.
As Dr. Steinbrecher said in
http://archive.ambermd.org/201005/0129.html, I have to extrapolation
from 0.05 and 0.95 outwards in softcore step.
But curve near 0.95 was very steep and should be a considerable error
if I simply use a linear extrapolation.
Is there any good scheme for extrapolation in this case?

And, I extract MBAR data using the script in
http://archive.ambermd.org/201105/0253.html, but I don't know how to
feed the data to pymbar. Is there any tutorial?

Here is a section of mbar data in one of my output file. The slope of
curve near 0.95 is steep.

MBAR Energy analysis:
Energy at 0.0500 = -21344.6480
Energy at 0.1000 = -21345.4438
Energy at 0.1500 = -21346.0208
Energy at 0.2000 = -21346.4153
Energy at 0.2500 = -21346.6488
Energy at 0.3000 = -21346.7321
Energy at 0.3500 = -21346.6666
Energy at 0.4000 = -21346.4448
Energy at 0.4500 = -21346.0495
Energy at 0.5000 = -21345.4508
Energy at 0.5500 = -21344.6019
Energy at 0.6000 = -21343.4296
Energy at 0.6500 = -21341.8168
Energy at 0.7000 = -21339.5673
Energy at 0.7500 = -21336.3242
Energy at 0.8000 = -21331.3574
Energy at 0.8500 = -21322.8808
Energy at 0.9000 = -21305.0181
Energy at 0.9500 = -21242.7100

Best Regard!

Denis

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Received on Thu Aug 16 2012 - 09:00:03 PDT
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