Re: [AMBER] Plotting heat maps in AMBER aMD simualtions

From: filip fratev <>
Date: Wed, 11 Dec 2013 10:18:20 -0800 (PST)

Hi Jason,
Thanks for your answer, now it is much clear! What I worry about is the units in amd.log. As Dan have already mentioned in this topic:
"I believe that the potential/dihedral energies are reported in units
of kcal/mol, but the boost energies are reported in units of KT."

Is that correct? and also is that the reason for problems described here by Alonso?:


On Wednesday, December 11, 2013 7:55 PM, Jason Swails <> wrote:
On Wed, Dec 11, 2013 at 10:56 AM, filip fratev <>wrote:

> Hi all,
> Recently I asked about the progress of the aMD tutorial and the python
> script to reweight and plot the energies. Is there any progress?

Not to my knowledge.  I think the people originally responsible for the aMD
implementation have moved on and may not be as regular contributors
anymore, so I'm not sure what the status of this is.

> I think that there are still some open questions, which not received clear
> answer for me:
> May ask for some very simple guide about reweighting procedure? I'd like
> one of my students to make some python script but want to be sure that use
> the correct formula and approach.

The formula for reweighting can be found in the original aMD paper, though.
You would just need to find the weight for each point (using the output
from the aMD log). numpy provides an option to supply point weights in the
'histogram' function, which seems about as straightforward as possible.
You could, of course, implement this in pure python, but numpy will be
much faster.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Dec 11 2013 - 10:30:02 PST
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