[gmx-developers] Brownian Dynamics and Kinetic energy

Paula Petrone ppetrone at stanford.edu
Fri Aug 12 20:45:19 CEST 2005


I have some inconsistency when calculating the kinetic energy of a 
Brownian Dynamics system from:

1) the velocities in the output velocity.xvg
2) the energy printed in energy.xvg

for the trajectory.
These two look pretty different. So I set the temperature to zero, I 
set the Removal of Center of Mass translation to linear and/or zero. I 
used a very small system with only bonded interactions. I did not use 
constraints. I wonder if there is any other correction done. Maybe for 
the kinetic energy of the center of mass?
I checked in the manual and for stochastic dynamics there is a friction 
correction of the velocities. Is this correction also done in Brownian 
Dynamics -after the calculation of kinetic energy?.

Some ideas?

Thank you in advance.

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