AMBER Archive (2008)

Subject: Re: AMBER: NMODE units and hrmax value for Langevine modes

From: David A. Case (case_at_scripps.edu)
Date: Thu Jun 05 2008 - 13:12:24 CDT

On Wed, Jun 04, 2008, Yang, Lee-Wei wrote:

> Thank you for the useful reply Dave. I wonder if there is a 'ok' hrmax value
> (for all the heavy atoms) that I can use to get a first approximation.
> Also, what is the value 0.2 for hydrogen? means 20% of its surface area
> being covered by solvent? therefore the value of hrmax has its maxima unity
> and minimum zero? It will be very kind of you to forward me a pointer
> regarding this. Thank you in advance.

It's been a *long* time since I personally did Langevin mode calculations. I
don't really remember how/why we decided on the option to reduce the friction
for hydrogens. You might want to study papers by Rich Pastor on this subject.
For example:

%A R.M. Venable
%A R.W. Pastor
%T Frictional models for stochastic simulations of proteins
%J Biopolymers
%V 27
%P 1001-14
%D 1988

%A R.W. Pastor
%A M. Karplus
%T Parametrization of the friction constant for stochastic simulations of
polymers
%J J. Phys. Chem.
%V 92
%P 2636-41
%D 1988

Beyond this, I think you are on your own: you will either have to find
literature on the best values, or experiment to see what happens. It might
help to try a citation search on the papers listed above.

...regards...dac

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