Re: [AMBER] How to generate Free energy landscape for amber trajectory?

From: Carlos Simmerling <>
Date: Wed, 7 Aug 2019 05:58:07 -0600

The first thing to do is to choose the coordinate or descriptor along which
free energy will be estimated. That is something that you will need to
decide based on your knowledge of the system and what you are trying to
study. Next you will calculate (probably in cpptraj) the value of that
coordinate for each frame of the trajectory, then histogram these values.
In order to convert to free energy you need to ensure that this histogram
represents an equilibrium ensemble. This is very important and should not
be skipped. The minimum you would want to do is to break your trajectory
into subsets (such as first and second half, or perhaps smaller chunks) and
make sure the histograms match. This isn't sufficient but is really the
minimum you should do. Independent runs from independent initial
coordinates is more reliable.

You should also plot this data stream to get a sense of the timescale of
the dynamics along this coordinate. Ideally you will see many transitions
back and forth along the full range of the coordinate. If not, this
suggests that calculation of free energy is not possible using just this
data set. More detailed analysis would involve calculation of correlation
times for this coordinate.

Assuming the data subsets match well, you can convert the histogram bins to
free energy by using a script that calculates
 where Pi is the population in bin at coordinate value i and P0 is the
population of the most populated bin. This sets the minimum free energy at
0 (which is arbitrary).

Next you can repeat this for your data subsets to calculate the
uncertainties in the free energy values. Don't neglect this part, or you
may generate very misleading data if the populations are not converged. I
microsecond may be enough, or it may be far too short. It depends on your
system and the timescale of the motions along the coordinate you selected.
This is why viewing the time dependence of the calculated coordinate values
is important.

On Tue, Aug 6, 2019, 11:18 PM M RCC <> wrote:

> Dear Amber users,
> I have performed amber simulation for 1 microsecond using pmemd module. I
> want to generate free energy landscape from the trajectory. Is there any
> software tools/tutorials /protocols available for this?
> (I have generated in Gromacs trajectory, But no tutorials are available for
> this in Amber)
> Thank You
> _______________________________________________
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Received on Wed Aug 07 2019 - 05:00:03 PDT
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