AMBER Archive (2005)Subject: AMBER: Separating solvent and solute energy in the microcanonical mode
From: Mey Khalili (ms284_at_cornell.edu)
Date: Thu Mar 17 2005 - 16:50:09 CST
Hi,
I am trying to estimate the extent to which the total energy is
conserved in microcanonical mode in AMBER. I ran Ala10 in a box of
water in the NVE mode, without any coupling to the Berendsen bath as I
know from the AMBER archive that this method does not keep the total
energy as constant as the NVE mode.
I ran the system for 90ps and then monitored the total, potential and
kinetic energy of the entire system. The drift in the total energy is
0.5% of the kinetic and 0.6% of the potential energy. But this is the
TOTAL energy of the solvent plus the protein. How do I extract the
protein's potential, kinetic and total energy to see to what extent the
total energy of the protein is conserved?
Thanks
Mey
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
|