AMBER Archive (2005)

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

From: Mey Khalili (ms284_at_cornell.edu)
Date: Thu Mar 17 2005 - 17:11:48 CST

  Even so, can you tell me how to calculate each component separately?

  Thanks
 Mey

> 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: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
>
>
> 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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