# Re: [AMBER] MBAR calculation

Date: Thu, 16 Aug 2012 11:50:57 -0400

Hi Denis,

I'm not exactly sure how those scripts deal with the data (do they run an
MBAR calculation?), but the MBAR formalism contains an intrinsic method for
extrapolation to unsampled states. The only requirement is that you are
able to evaluate the energy (in practice, the energy difference) in the
desired state. This is covered rather extensively in Shirts and Chodera's
paper on the subject.

In my experience this can be a little tricky with softcore calculations
because you have to create endpoint prmtops and then re-evaluate the
trajectories with the correct number of atoms (so one endpoint may actually
need a proper dummy atom).

As for pymbar, you probably have to modify one of the example scripts and
then add the extra states. There may be some new tutorials with the new
beta release of 2.0, but I haven't spent too much time with it yet.

Regards,
Brian

On Thu, Aug 16, 2012 at 11:33 AM, Liu Denis <cndenis.gmail.com> wrote:

> 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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