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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 17 2011 - 19:00:03 PDT
