AMBER Archive (2009)

Subject: Re: [AMBER] diffusion coeficients

From: felix (vitor.felix_at_ua.pt)
Date: Fri Jul 17 2009 - 08:41:43 CDT

Dear Prof. Case
Thank you very much for your prompt help. Usually in my simulations
including free energy calculations I use the following option NTT=3,
gamma_ln =1.0. The gamma_ln =3.0 was a typo.

Sincerely yours

Vitor Felix

case wrote:
> On Fri, Jul 17, 2009, felix wrote:
>
>
>> I would like to know if the langevin thermostat (3.0)
>> is appropriate to estimate hydrodynamic properties such as diffusion
>> coefficients. Otherwise we have to use ntt=2
>>
>
> Neither option listed above will work in any simple fashion, since all
> thermostats modify Newtonian dynamics. Here is a recent paper that discusses
> one way to extract diffusion constants from simulations (using ntt=0):
>
> %A V. Wong
> %A D.A. Case
> %T Evaluating Rotational Diffusion from Protein MD Simulations
> %J J. Phys. Chem. B
> %V 112
> %P 6013-6024
> %D 2008
>
> The above uses explicit solvent simulations. If you wanted to use langevin
> dynamics and implicit solvent, you might start from a very old paper:
>
> %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
>
> But you would need a value of gamma_ln very different from 3, and probably
> would have to do a fair amount calibration as well. (I have not tried this
> method myself....)
>
> ...dac
>
>
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> 

-- 
*************************************
Vitor Felix
Department of Chemistry
University of Aveiro
3810-193 Aveiro, Portugal
Tel: 351 234 370 200 ext: 22102
http://molecular-modeling.dq.ua.pt

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