Dear Dr. Case,
Thanks for the heads up regarding the use of thermostats! Makes sense that
giving the particles an artificial push to maintain temp will affect their
motion over time.
Dean
On 10/17/11 8:32 PM, "David A. Case" <case.biomaps.rutgers.edu> wrote:
>On Mon, Oct 17, 2011, Dean Cuebas wrote:
>
>> I am simulating some organic solvents using PME MD in with Langevin
>> thermostat.
>>
>> Are there any flags I need to watch out for while determining bulk
>> properties, like density, Diffusion coefficient, etc?
>
>Any thermostat will adversely affect time-dependent properties (such as
>diffusion coefficients), and a Langevin thermostat is likely to be
>especially
>suspect. You need to be able to run NVE simulations for such
>calculations;
>time-independent quantities (such as the density) should be fine with a
>thermostat.
>
>There is some evidence that a *weak* Berendsen thermostat can be used in
>explorations of dynamical properties (see reference below), but my own
>preference is to not mess with Newton's equations.
>
>%A A. Mudi
>%A C. Chakravarty
>%T Effect of the Berendsen thermostat on the dynamical properties of water
>%J Mol. Phys.
>%V 102
>%P 681-685
>%D 2004
>
>...dac
>
>
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Received on Mon Oct 17 2011 - 20:30:03 PDT
