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193 lines
8.4 KiB
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<HR>
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<H3>run_style command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>run_style style args
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</PRE>
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<UL><LI>style = <I>verlet</I> or <I>respa</I>
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<PRE> <I>verlet</I> args = none
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<I>respa</I> args = N n1 n2 ... keyword values ...
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N = # of levels of rRESPA
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n1, n2, ... = loop factor bewteen rRESPA levels (N-1 values)
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zero or more keyword/value pairings may be appended to the loop factors
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keyword = <I>bond</I> or <I>angle</I> or <I>dihedral</I> or <I>improper</I> or
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<I>pair</I> or <I>inner</I> or <I>middle</I> or <I>outer</I> or <I>kspace</I>
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<I>bond</I> value = M
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M = which level (1-N) to compute bond forces in
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<I>angle</I> value = M
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M = which level (1-N) to compute angle forces in
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<I>dihedral</I> value = M
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M = which level (1-N) to compute dihedral forces in
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<I>improper</I> value = M
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M = which level (1-N) to compute improper forces in
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<I>pair</I> value = M
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M = which level (1-N) to compute pair forces in
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<I>inner</I> values = M cut1 cut2
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M = which level (1-N) to compute pair inner forces in
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cut1 = inner cutoff between pair inner and
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pair middle or outer (distance units)
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cut2 = outer cutoff between pair inner and
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pair middle or outer (distance units)
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<I>middle</I> values = M cut1 cut2
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M = which level (1-N) to compute pair middle forces in
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cut1 = inner cutoff between pair middle and pair outer (distance units)
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cut2 = outer cutoff between pair middle and pair outer (distance units)
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<I>outer</I> value = M
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M = which level (1-N) to compute pair outer forces in
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<I>kspace</I> value = M
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M = which level (1-N) to compute kspace forces in
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>run_style verlet
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run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4
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run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Choose the style of time integrator used for molecular dynamics
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simulations performed by LAMMPS.
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</P>
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<P>The <I>verlet</I> style is a velocity-Verlet integrator.
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</P>
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<P>The <I>respa</I> style implements the rRESPA multi-timescale integrator
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<A HREF = "#Tuckerman">(Tuckerman)</A> with N hierarchical levels, where level 1 is
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the innermost loop (shortest timestep) and level N is the outermost
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loop (largest timestep). The loop factor arguments specify what the
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looping factor is between levels. N1 specifies the number of
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iterations of level 1 for a single iteration of level 2, N2 is the
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iterations of level 2 per iteration of level 3, etc. N-1 looping
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parameters must be specified.
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</P>
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<P>The <A HREF = "timestep.html">timestep</A> command sets the timestep for the
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outermost rRESPA level. Thus if the example command above for a
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4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep
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would be 8x smaller or 0.5 fmsec. All other LAMMPS commands that
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specify number of timesteps (e.g. <A HREF = "neigh_modify.html">neigh_modify</A>
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parameters, <A HREF = "dump.html">dump</A> every N timesteps, etc) refer to the
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outermost timesteps.
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</P>
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<P>The rRESPA keywords enable you to specify at what level of the
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hierarchy various forces will be computed. If not specified, the
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defaults are that bond forces are computed at level 1 (innermost
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loop), angle forces are computed where bond forces are, dihedral
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forces are computed where angle forces are, improper forces are
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computed where dihedral forces are, pair forces are computed at the
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outermost level, and kspace forces are computed where pair forces are.
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The inner, middle, outer forces have no defaults.
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</P>
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<P>The <I>inner</I> and <I>middle</I> keywords take additional arguments for
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cutoffs that are used by the pairwise force computations. If the 2
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cutoffs for <I>inner</I> are 5.0 and 6.0, this means that all pairs up to
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6.0 apart are computed by the inner force. Those between 5.0 and 6.0
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have their force go ramped to 0.0 so the overlap with the next regime
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(middle or outer) is smooth. The next regime (middle or outer) will
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compute forces for all pairs from 5.0 outward, with those from 5.0 to
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6.0 having their value ramped in an inverse manner.
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</P>
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<P>Only some pair potentials support the use of the <I>inner</I> and <I>middle</I>
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and <I>outer</I> keywords. If not, only the <I>pair</I> keyword can be used
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with that pair style, meaning all pairwise forces are computed at the
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same rRESPA level. See the doc pages for individual pair styles for
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details.
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</P>
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<P>When using rRESPA (or for any MD simulation) care must be taken to
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choose a timestep size(s) that insures the Hamiltonian for the chosen
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ensemble is conserved. For the constant NVE ensemble, total energy
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must be conserved. Unfortunately, it is difficult to know <I>a priori</I>
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how well energy will be conserved, and a fairly long test simulation
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(~10 ps) is usually necessary in order to verify that no long-term
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drift in energy occurs with the trial set of parameters.
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</P>
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<P>With that caveat, a few rules-of-thumb may be useful in selecting
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<I>respa</I> settings. The following applies mostly to biomolecular
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simulations using the CHARMM or a similar all-atom force field, but
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the concepts are adaptable to other problems. Without SHAKE, bonds
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involving hydrogen atoms exhibit high-frequency vibrations and require
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a timestep on the order of 0.5 fmsec in order to conserve energy. The
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relatively inexpensive force computations for the bonds, angles,
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impropers, and dihedrals can be computed on this innermost 0.5 fmsec
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step. The outermost timestep cannot be greater than 4.0 fmsec without
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risking energy drift. Smooth switching of forces between the levels
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of the rRESPA hierarchy is also necessary to avoid drift, and a 1-2
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angstrom "healing distance" (the distance between the outer and inner
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cutoffs) works reasonably well. We thus recommend the following
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settings for use of the <I>respa</I> style without SHAKE in biomolecular
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simulations:
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</P>
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<PRE>timestep 4.0
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run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 8.0 10.0 outer 4
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</PRE>
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<P>With these settings, users can expect good energy conservation and
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roughly a 2.5 fold speedup over the <I>verlet</I> style with a 0.5 fmsec
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timestep.
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</P>
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<P>If SHAKE is used with the <I>respa</I> style, time reversibility is lost,
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but substantially longer time steps can be achieved. For biomolecular
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simulations using the CHARMM or similar all-atom force field, bonds
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involving hydrogen atoms exhibit high frequency vibrations and require
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a time step on the order of 0.5 fmsec in order to conserve energy.
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These high frequency modes also limit the outer time step sizes since
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the modes are coupled. It is therefore desireable to use SHAKE with
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respa in order to freeze out these high frequency motions and increase
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the size of the time steps in the respa hierarchy. The following
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settings can be used for biomolecular simulations with SHAKE and
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rRESPA:
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</P>
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<PRE>fix 2 all shake 0.000001 500 0 m 1.0 a 1
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timestep 4.0
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run_style respa 2 2 inner 1 4.0 5.0 outer 2
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</PRE>
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<P>With these settings, users can expect good energy conservation and
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roughly a 1.5 fold speedup over the <I>verlet</I> style with SHAKE and a
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2.0 fmsec timestep.
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</P>
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<P>For non-biomolecular simulations, the <I>respa</I> style can be
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advantageous if there is a clear separation of time scales - fast and
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slow modes in the simulation. Even a LJ system can benefit from
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rRESPA if the interactions are divided by the inner, middle and outer
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keywords. A 2-fold or more speedup can be obtained while maintaining
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good energy conservation. In real units, for a pure LJ fluid at
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liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
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Kcal/mol, the following settings seem to work well:
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</P>
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<PRE>timestep 36.0
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run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3
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</PRE>
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<P><B>Restrictions:</B> none
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</P>
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<P>Whenever using rRESPA, the user should experiment with trade-offs in
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speed and accuracy for their system, and verify that they are
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conserving energy to adequate precision.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "timestep.html">timestep</A>, <A HREF = "run.html">run</A>
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</P>
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<P><B>Default:</B>
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</P>
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<PRE>run_style verlet
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</PRE>
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<HR>
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<A NAME = "Tuckerman"></A>
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<P><B>(Tuckerman)</B> Tuckerman, Berne and Martyna, J Chem Phys, 97, p 1990
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(1992).
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</P>
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</HTML>
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