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Force in MODELLER is obtained by equating the objective function
with internal energy in kcal/mole. The atomic masses are all set to
that of C
(MODELLER unit is kg/mole). The initial velocities
at a given temperature are obtained from a Gaussian random number
generator with a mean and standard deviation of:
where
is the Boltzmann constant,
is the mass of one C
atom,
and the velocity is expressed in angstroms/femtosecond.
The Newton's equations of motion are integrated by the Verlet
algorithm [#!Ver67!#]:
where velocities
are for
and positions
for
. Parameter
is a scaling factor so that
positions are expressed in angstroms, time in femtoseconds, and
velocities in angstroms/femtosecond, given that the objective function
is in kcal/mole and atomic mass in kg/mole. In addition, velocity is
capped at a maximum value, before calculating the shift, such that the
maximal shift along one axis can only be CAP_ATOM_SHIFT. The
velocities can be equilibrated every EQUILIBRATE steps to
stabilize temperature. This is achieved by scaling the velocities
with a factor
:
where
is the current kinetic energy of the system.
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Bozidar BJ Jerkovic
2001-12-21