Usage of velDCDfile and forceDCDfile keywords in viscosity calculations

From: Debashis Kundu (
Date: Mon Dec 14 2015 - 00:34:56 CST

Hello NAMD users,

I am trying to calculate viscosity using Equilibrium MD simulation (NPT) by
applying MSSD (mean squared stress displacement) approach. For that, I have
to calculated velocity and forces acting on atoms. Presently, I calculate
velocity and forces by extracting the coordinates from DCDfile and
subsequently apply verlet algorithm. There are options to use velDCDfile
and forceDCDfile keywords in NAMD to extract velocity and forces from the
system. Will I get better result if I use these keywords instead of
calculating them from coordinate DCD file?



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