If you use T-WHAM, PT-WHAM, or MBAR, I suspect you are going to have
to convert your simulation data into the format that these programs
accept. MBAR is highly regarded, from a technical point of view.
These are general and powerful programs, but they are not customised
to handle AMBER data, and may or may not handle PMFs conveniently.
The conversion should not be very difficult if you are familiar with
awk or excell.
I recall the Grossfield Lab also has a version of WHAM you can use:
http://membrane.urmc.rochester.edu/content/wham
I don't know if there is a version of WHAM that is supposed to be
easier to use for AMBER data. (Sorry I'm not an AMBER user.)
--- WHAM rant comming: ---
Do you really need WHAM?
I'm not sure what you are trying to do. I am assuming that you are
trying to generate a PMF (potential of mean force), or compute an
average or a fluctuation.
If this is the case, then I would advocate that you first do it
directly using only the data collected during your simulations at the
temperature of interest (and ignoring data from the other
temperatures). In other words, ignore WHAM and try calculating
whatever you want to calculate directly. (IE. you can generate a
reasonable PMF by generating a histogram of the quantity of interest
from your single-temperature data, and calculating it's negative
logarithm *kB*T. If you are trying to calculate solvation free-energy
differences, try the Zwanzig relation used in free-energy
perturbation.)
You can run WHAM later to generate smoother, nicer looking results.
But if replica exchange was working and your simulations converged,
then using WHAM should not make a qualitative difference. Our group
uses WHAM extensively. It's easy to mess up the energy units in WHAM,
or make other mistakes that can distort the results. So even if you
intend to use WHAM, be sure to compare your fancy WHAM results with
what you get by doing it the ordinary way. WHAM is nice, but in most
cases it's not likely to make your results more publishable.
Rant over.
Cheers.
Andrew
If you want to understand the algorithm better, I like the description
given in the Chodera paper. The first half of that paper has a very
nice mathematical description of the original WHAM algorithm. The
second half describes how he modified it to handle replica exchange
data, although nowadays I think Chodera also sometimes advocates using
MBAR. (I'm somewhat jealous. Our lab was planning to release our own
version of WHAM. It will happen one day.)
On Tue, Sep 6, 2011 at 8:49 AM, Brian Radak <radak004.umn.edu> wrote:
> I am not an expert in temperature replica exchange, but I do make heavy use
> of WHAM and its close cousin MBAR. The papers that come to my mind are
> (there are perhaps others):
>
> Gallichio, et al J Phys Chem B 2005, 109, 6722. - T-WHAM
>
> Chodera, et al J Chem Theory Comput 2007, 3, 26. - PT-WHAM
>
> Shirts and Chodera J Chem Phys 2008, 129, 124105 - MBAR
>
> Happy reading,
> Brian
>
> On Tue, Sep 6, 2011 at 10:20 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
>>
>> Dear Sir/Madam,
>> Any tutorial to teach us how to get PMF energy profile from Replica
>> Exchange Simulations? I learn from previous message in this forum that I
>> can use WHAM, how to incorporate the temperature factor in the analysis?
>> I studied tutorial a7, but it did not include the energy analysis part.
>> Any reference should I read?
>> Best regards,
>> Catherine
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>>
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Wright-Rieman Hall 101
> Graduate Program in Chemical Physics : 610 Taylor Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
> radak004.umn.edu :
> radakb.biomaps.rutgers.edu
> ====================================================================
> Sorry for the multiple e-mail addresses, just use the institute appropriate
> address.
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Received on Tue Sep 06 2011 - 16:30:02 PDT
