[gmx-users] Berendsen Temperature Coupling and Heat
Daniel S. Han
dsh2002 at med.cornell.edu
Tue Jul 29 22:49:19 CEST 2008
Hello,
I am running a steered MD simulation in an NPT ensemble using Berendsen
thermostats. I expect that my system could heat up due to the external
forces, and this heat would eventually be absorbed by the heat bath.
I thought I could get an estimate of the heat released by looking at the
Temperature (T) and lambda values (velocity scaling factors) available
in the gromacs energy output files, but I wasn't sure I was calculating
it correctly.
Here's the algorithm I thought might work:
at every time step, we have a Temperature (T) and a Lambda (L) taken
from the edr output file.
Where we can calculate the kinetic energy at any step as:
Kinetic Energy (KE) = .5 * N_degrees_of_freedom * K_boltzman * T
(which I'll call KE_output)
If I understand correctly, KE_output is the result after scaling by
Lambda^2. So if there were no temperature scaling, then the kinetic
energy would be equal to:
KE_no_scaling = KE_output / (lambda*lambda)
Thus the heat exchanged between the system and the bath is:
Heat = KE_output - KE_no_scaling
where if heat is negative, it means that heat was released by the system
and absorbed by the bath.
Using this algorithm I found some odd results, where I found that both
my Steered MD simulations and a simulation of the same system without
external forces tended to absorb heat.
I can post more details of that later, but for now, if anyone has any
corrections/comments to this line of thought, it would be much appreciated.
Thanks in advance,
Danny.
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