AMBER Archive (2009)

Subject: Re: [AMBER] analysis on Amber

From: Thomas Cheatham (
Date: Sat Mar 07 2009 - 12:18:58 CST

> I'm interested in evaluating thermophysical and rheological properties of
> n-alkanes and binary mixtures of n-alkanes. I performed md simulations using
> Amber 10 v. and I want to do analysis with my Amber trajectory files. My
> aim is to get Self Diffusion coefficents from calculating MSD and velocity

Why do you need both velocity autocorrelation and MSD? They should be
equivalent, however you could write a Perl script or a small program to
read the velocities and perform the necessary analysis. You can dump the
velocity information (like dumping the trajectory) with the NTWV parameter
in the &cntrl namelist.

> autocorrelation functions and to get shear viscosity from calculating the
> autocorrelation functions of the stress tensors. For this reason, I
> searched Amber manuals, tutorials and mail archives in order to have enough

As mentioned numerous times in e-mail, to do this you will have to dig
into the Ewald code and figure out how to dump the stress tensors, or
alternatively you have to convince someone else to do this. As there have
been very few responses to your queries on the reflector, likely you will
have to do this yourself. As a first step, I would consult the primary
literature and go back to the earlier papers on calculating stress tensors
of water. Once you understand this, then I would interrogate a code that
calculates this already like GROMACS and then look into AMBER...


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