[gmx-developers] Brownian Dynamics and Kinetic energy
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?.
Thank you in advance.
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