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@ -46,26 +46,30 @@ interaction with a background implicit solvent. Used with <A HREF = "fix_nve.ht
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nve</A>, this command performs Brownian dynamics (BD), since
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the total force on each atom will have the form:
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</P>
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<PRE>F = Fc + Ff + Fr
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<PRE>F = Fc + Ff + Fr
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Ff = - (m / damp) v
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Fr is proportional to sqrt(Kb T m / (dt damp))
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</PRE>
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<P>Fc is the conservative force computed via the usual inter-particle
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interactions (<A HREF = "pair_style.html">pair_style</A>,
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<A HREF = "bond_style.html">bond_style</A>, etc).
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</P>
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<P>The Ff and Fr terms are added by this fix. Ff = - gamma v and is a
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frictional drag or viscous damping term proportional to the particle's
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velocity. Gamma for each atom is computed as m/damp, where m is the
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mass of the particle and damp is the damping factor specified by the
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user.
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<P>The Ff and Fr terms are added by this fix.
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</P>
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<P>Ff is a frictional drag or viscous damping term proportional to the
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particle's velocity. The proportionality constant for each atom is
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computed as m/damp, where m is the mass of the particle and damp is
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the damping factor specified by the user.
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</P>
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<P>Fr is a force due to solvent atoms at a temperature T randomly bumping
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into the particle. As derived from the fluctuation/dissipation
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theorem, its magnitude is proportional to sqrt(T m / dt damp), where T
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is the desired temperature, m is the mass of the particle, dt is the
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timestep size, and damp is the damping factor. Random numbers are
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used to randomize the direction and magnitude of this force as
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described in <A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used
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(instead of a Gaussian random number) for speed.
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theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
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dt damp), where Kb is the Boltzmann constant, T is the desired
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temperature, m is the mass of the particle, dt is the timestep size,
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and damp is the damping factor. Random numbers are used to randomize
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the direction and magnitude of this force as described in
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<A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used (instead of
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a Gaussian random number) for speed.
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</P>
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<P>Note that the thermostat effect of this fix is applied to only the
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translational degrees of freedom for the particles, which is an
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@ -37,26 +37,30 @@ interaction with a background implicit solvent. Used with "fix
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nve"_fix_nve.html, this command performs Brownian dynamics (BD), since
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the total force on each atom will have the form:
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F = Fc + Ff + Fr :pre
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F = Fc + Ff + Fr
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Ff = - (m / damp) v
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Fr is proportional to sqrt(Kb T m / (dt damp)) :pre
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Fc is the conservative force computed via the usual inter-particle
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interactions ("pair_style"_pair_style.html,
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"bond_style"_bond_style.html, etc).
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The Ff and Fr terms are added by this fix. Ff = - gamma v and is a
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frictional drag or viscous damping term proportional to the particle's
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velocity. Gamma for each atom is computed as m/damp, where m is the
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mass of the particle and damp is the damping factor specified by the
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user.
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The Ff and Fr terms are added by this fix.
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Ff is a frictional drag or viscous damping term proportional to the
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particle's velocity. The proportionality constant for each atom is
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computed as m/damp, where m is the mass of the particle and damp is
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the damping factor specified by the user.
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Fr is a force due to solvent atoms at a temperature T randomly bumping
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into the particle. As derived from the fluctuation/dissipation
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theorem, its magnitude is proportional to sqrt(T m / dt damp), where T
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is the desired temperature, m is the mass of the particle, dt is the
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timestep size, and damp is the damping factor. Random numbers are
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used to randomize the direction and magnitude of this force as
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described in "(Dunweg)"_#Dunweg, where a uniform random number is used
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(instead of a Gaussian random number) for speed.
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theorem, its magnitude as shown above is proportional to sqrt(Kb T m /
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dt damp), where Kb is the Boltzmann constant, T is the desired
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temperature, m is the mass of the particle, dt is the timestep size,
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and damp is the damping factor. Random numbers are used to randomize
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the direction and magnitude of this force as described in
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"(Dunweg)"_#Dunweg, where a uniform random number is used (instead of
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a Gaussian random number) for speed.
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Note that the thermostat effect of this fix is applied to only the
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translational degrees of freedom for the particles, which is an
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