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From: Ross Walker <ross.rosswalker.co.uk>

Date: Mon, 18 Sep 2006 08:52:23 -0700

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

minimisation).

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

Ross

/\

\/

|\oss Walker

| HPC Consultant and Staff Scientist |

| San Diego Supercomputer Center |

| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |

| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not

be read every day, and should not be used for urgent or sensitive issues.

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Received on Wed Sep 20 2006 - 06:07:10 PDT

Date: Mon, 18 Sep 2006 08:52:23 -0700

Dear Fenghui,

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

minimisation).

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.

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.

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

Ross

/\

\/

|\oss Walker

| HPC Consultant and Staff Scientist |

| San Diego Supercomputer Center |

| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |

| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not

be read every day, and should not be used for urgent or sensitive issues.

-----------------------------------------------------------------------

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Sep 20 2006 - 06:07:10 PDT

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