Re: [AMBER] understanding results

From: David A Case <>
Date: Thu, 18 May 2017 09:35:19 -0400

On Wed, May 17, 2017, Carlos Romero wrote:

> I want to know how changes the response of one protein when it is in
> diferent pH.
> My know about Molecular Dynamics is that resulting trajectories are the
> possibles conformations of a molecule after being applied some energy, many
> of them are not possible because wrong conformations, but some of them are
> probably right. Among these structures, is one with the lowest potential
> energy, which is the most probably in nature.

This is not correct. There are always thermal fluctuations, and an
equilibrated MD simulation should sample the correct distribution. There are
no "right" or "wrong" conformations, just ones that occur more frequently or
less frequently.

If you wish to extract snapshots from MD simulations, say to perform a docking
calculation, it would be more realistic to choose random ones (and certainly
more than one), than to choose the frame with the lowest potential energy.


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Received on Thu May 18 2017 - 07:00:03 PDT
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