Re: AMBER: comparison of MD trajectories recorded with pmemd and sander

From: Gustavo Seabra <>
Date: Thu, 18 Dec 2008 09:58:13 -0500

Hi Thérèse,

I suppose at this point you must already be tired of reading so many
answers to your question, but I wanted to add just one comment that
hasn't been clearly addressed in the replies I've seen:

On Wed, Dec 17, 2008 at 9:04 AM, Thérèse Malliavin wrote:
> But, I am concerned by the following problem. Molecular modeling studies are
> often based on the comparison of MD trajectories run with several
> conditions.

This is not strictly correct. As you already know at this point, it is
unrealistic to expect the trajectories to be exactly the same, for the
reasons that have been exhaustively discussed here. As Ross pointed
out, what you should be looking for are the ensemble-averaged
properties, *not* the trajectory itself. As long as the implementation
is correct, the two different trajectories should differ just by the
order in which they visit different regions of the phase-space. But,
if the simulations are long enough,[*] they should in the end all
visit each region the same number of times yielding the same average
properties, given the conditions are all the same, independently of
the program used.

[*] defining what does "simulations are long enough" mean is a
completely different issue...
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Received on Fri Dec 19 2008 - 01:18:01 PST
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