Viscosity Calculation using EMD

From: Gaurab Sarkar (
Date: Mon Dec 14 2015 - 13:22:02 CST

Hello NAMD Users,

I'm trying to predict viscosity of compounds using Einstein relation for
viscosity from Equilibrium Molecular Dynamics simulations. As I'm trying to
calculate the Mean Squares Stress Displacement from the .dcd file obtained
using matdcd functionality of Matlab, I'm posed with a few problems. I'm
proceeding to calculate the stress terms, which includes velocity and
force, from the coordinates in the .dcd file. With increase in temperature
of simulation the calculated viscosity is increasing. Is this because the
stress calculation is obtained from coordinates in the dcd file and with
increase in temperature the simulated box size increases? Is it also
because with increase in temperature the resulted system gets relaxed which
means the molecules are farther away from each other which ultimately
affects the velocity and force calculation in the stress displacement term
resulting in higher viscosity with increase in temperature?

 Thanks and Regards.
 Gaurab Sarkar

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