AMBER: Separating solvent and solute energy in the microcanonical mode

From: Mey Khalili <>
Date: Thu, 17 Mar 2005 17:50:09 -0500 (EST)


  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?



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Received on Thu Mar 17 2005 - 22:53:00 PST
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