It does indeed.
Thank you
On 22 Mar 2013, at 17:06, David A Case <case.biomaps.rutgers.edu> wrote:
> 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 - 14:00:03 PDT
