On Fri, Mar 22, 2013, George Tzotzos wrote:
>
> I read in J. Chem. Phys. 105 (1) p.299 "In the Langevin dynamics
> formalism, the explicit solvent degrees of freedom are eliminated from
> the nonequilibrium thermodynamic description"
>
> In Amber simulations Langevin dynamics (ntt=3) are run in explicit solvent.
Different meanings of the words "Langevin dynamics", depending on context.
The first paragraph might be better written "In one example of a Langevin
dynamics formalism,...."
The second paragraph might more correctly refer to a "Langevin thermostat"
or "Langevin-inspired dynamics" rather than to "Langevin dynamics".
Generally, whether in implicit or explicit solvent, Amber simulations with
ntt=3 are run with a friction coefficient that is much smaller than the
actual friction of water.
....hope this helps...dac
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Received on Fri Mar 22 2013 - 13:30:05 PDT
