[gmx-users] two questions on multiple simulations and stochastic dynamics

[Berk Hess]

>2) I am using the stochastic integrator in gmx3.0.5. I notice that there is 
>only the inverse friction constant used in mdp, does this mean that the 
>friction force here is only related to the friction coefficient of
>solvent molecules without considering the fraction of solute surface 
>exposed to the solvent? In GROMOS96 package, the friction force is related 
>to both. Since the friction coefficient of water is 91 (ps-1), what 
>parameter should be set for tau_t as inverse friction constant in 
>stochastic dynamics of biomolecules? Any help will be sincerely 
>appreciated!

But Gromos96 probably only calculates the friction coefficients once at the 
beginning
of the simulations, or am I wrong?

First there is not 'one' friction constant for water.
I suppose the number 91 (ps-1) is derived for to get the right diffusion 
constant
for a single water molecule. However there are many other motions, such as
libration and rotation.

What you would like is the correct dynamics for the parts of the protein 
that are
in contact with the solvent. This can never be accieved by using a single 
friction
constant for each particle. You would need a complete matrix (the Osene 
tensor)
which should also vary in time as groups become more or less exposed.

I guess the best thing to do would be to try several values and see if the 
timescales
of the properties that you are most interested in match.
Note that you can use different values for different groups, if you would 
like,
by using multiple temperature coupling groups.
The number 91 (ps-1) for water is useless here. The only case where you 
could
calclute things is for a single object moving though water, where you could 
use
the viscosity of the water. But you are not interested in the diffusion of 
the whole
protein through the solvent.
Sidechains are much too small and also interact with the protein.
To make matters worse, the water close to the protein is very ordered and 
much
more static than bulk water.

Berk.

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