AMBER Archive (2008)

Subject: Re: AMBER: Sources of disruption during NVE

From: Naser Alijabbari (
Date: Wed Oct 01 2008 - 20:10:43 CDT

Hi Gustavo,

I will try to explain what I am doing as best as I can.

>It's not clear what you mean by variability. How large is the difference?

I am comparing absorption coefficents btw .2-.7THz, and even here I am not
looking at absolute value of absorption coefficient but rather the position
of absorption peaks. Hence, the position of the peaks move or when there
should be a peak there is a trough or vice versa.

>Those simulation times are *very* small, and it's likely that your
>system isn't even close to equilibrating yet. How large is it? Did you
>look at any convergence properties to make sure it's OK? It is
>possible that the differences you see are just the consequence of not
>having an equilibrated ensemble.

The system has 12154 atoms (10500 water and 1654 protein 2TRX), and the
pressure, temperature, density and energy all seem to have equiliriated at
the end of 100ps density adjustment, based on looking at the output file (I
am using the Perl script provided in the tutorial). Therefore, the
production run for another 100ps should be equilibriated system.

>That's confusing... How different is "different"? In principle, to
>extract any observable from an md calculation you *must* average it
>over the simulation time. So, since you mention that the average
>gives about the same result, maybe they aren't as different... BTW,
>how did you do this averaging?

I feed my trajectory/.mdcrd file to ptraj to create a mass weighted
covariance matrix. My understanding was that this matrix is
created by averaging the variation in position of each atoms for the entire
time of production simulation. By averaging I meant using Simulink and
averaging the abosorption coefficient values afterwards.

>The discussions you mention are about a completely different thing (I
>believe). There, what's being discussed is energy conservation, which
>doesn't seem to be your issue.
So they are saying tolerance have to be tighter for longer simulation
periods, and I am guessing tighter tolerance mean longer calculation times.
For an NVE simulation w/ no translation removal during the simulation, are
there any other source of disturbance I am missing? I define translation
removal, pressure adjustment, and temperature adjustment as disturbances
because looking at the equations something is being either reset or
rescaled. So I thought SHAKE falls into that category. I am correct in
assuming volume is not touched when using NVE?

>You can, however, try to turn off SHAKE only for
>your solute, see the manual for "NOSHAKEMASK". If you do this, then
>you certainly must change your time step to something smaller than the
>vibrations of the bonds containing Hydrogens in your molecule.

I will definately look into "NOSHAKEMASK". I appreciate your response.

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