Re: AMBER: Separating solvent and solute energy in the microcanonical mode

From: Carlos Simmerling <>
Date: Thu, 17 Mar 2005 18:05:17 -0500

there is no reason that the total energy of the protein
should be conserved in the simulation. It is only the total
system energy that is constant- nothing is guaranteed
for components.

Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web:
Stony Brook, NY 11794-5115 E-mail:

Mey Khalili wrote:

> 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
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Received on Thu Mar 17 2005 - 23:53:00 PST
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