Re: RE: AMBER: potential energy

From: linfu <>
Date: Tue, 19 Sep 2006 09:44:18 +0800

Usually kineticn energy >0
   and potential energy <0
   and total erngy <0 for most system.
however if we met the case below
        kineticn energy >0
   and potential energy <0
   and total erngy >0 ******
does this MD simulation valid or not.

======= 2006-09-18 23:52:23 艇壓栖佚嶄亟祇=======

>Dear Fenghui,
>> For the results of MD,there are kinetic energy,
>> potential energy and relative energy. I think all
>> these should be relative quantity. Will you please
>> tell me in which state the protein has absolute 0
>> energy?
>The kinetic energy zero will be when the protein is at absolute zero kelvin.
>In other words when all the velocities are zero (or one is doing
>The potential energy zero is not within the phase space available to the
>protein. (I believe. It would be interesting to see if anyone can prove this
>mathematically for a given size protein). Essentially the zero point is when
>all of the bonds, angles and dihedrals are at their equilibrium geometries
>and the electrostatics and van der waals terms exactly balance. Suffice to
>say that unlike quantum mechanical calculations where all molecules /
>simulations share the same potential energy origin: All atoms seperated to
>infinity, this is not the case with classical MD calculations. Here the
>origin is different for different molecules / simulations. Hence you can
>only compare delta differences in relative energies.
>> After energy minimization, we get a protein
>> conformation with the lowest energy and this number is
>> usually negative. Can we difine the energy in this
>> conformation as 0 energy?
>As above the origin is a completely arbritrary position and is different for
>each molecule. So technically you can call any point you like the
>confirmation with zero energy. Note unless you know you are at the global
>minimum (which is unlikely for a protein since finding this is an NPComplete
>problem) then there is always the possibility that you could find structures
>of lower energy than what you have at the moment during your simulation.
>Minimisation has simply found you the nearest low energy minimum.
>> For the kinetics energy, it
>> should has some relation with the velocity, however
>> the initial velocity is produced randomly. Does this
>> means that the initial kinetic energy will be a random
>> value?
>No, the kinetic energy is a direct function of the temperature. Thus you set
>what you want the initial temperature to be and velocities are assigned
>randomly (weighted by a Boltzmann distribution) to the atoms such that the
>total kinetic energy results in the temperature you requested.
>You may want to refer to some graduate level texts on computational
>chemistry and statistical mechanics to make sure you understand the theory
>before attempting any major calculations.
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
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Received on Wed Sep 20 2006 - 06:07:14 PDT
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