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< title > dihedral_style command — LAMMPS 15 May 2015 version documentation< / title >
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2006-09-22 00:22:34 +08:00
2015-07-30 22:53:28 +08:00
2006-09-22 00:22:34 +08:00
2015-07-30 22:53:28 +08:00
2006-09-22 00:22:34 +08:00
2015-07-30 22:53:28 +08:00
2006-09-22 00:22:34 +08:00
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< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
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< li > dihedral_style command< / li >
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< a href = "http://lammps.sandia.gov" > Website< / a >
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< span id = "index-0" > < / span > < h1 > dihedral_style command< a class = "headerlink" href = "#dihedral-style-command" title = "Permalink to this headline" > ¶< / a > < / h1 >
< div class = "section" id = "syntax" >
< h2 > Syntax< a class = "headerlink" href = "#syntax" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > dihedral_style style
< / pre > < / div >
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< ul class = "simple" >
< li > style = < em > none< / em > or < em > hybrid< / em > or < em > charmm< / em > or < em > class2< / em > or < em > harmonic< / em > or < em > helix< / em > or < em > multi/harmonic< / em > or < em > opls< / em > < / li >
< / ul >
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< div class = "section" id = "examples" >
< h2 > Examples< a class = "headerlink" href = "#examples" title = "Permalink to this headline" > ¶< / a > < / h2 >
< div class = "highlight-python" > < div class = "highlight" > < pre > dihedral_style harmonic
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dihedral_style multi/harmonic
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dihedral_style hybrid harmonic charmm
< / pre > < / div >
< / div >
< / div >
< div class = "section" id = "description" >
< h2 > Description< a class = "headerlink" href = "#description" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Set the formula(s) LAMMPS uses to compute dihedral interactions
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between quadruplets of atoms, which remain in force for the duration
of the simulation. The list of dihedral quadruplets is read in by a
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< a class = "reference internal" href = "read_data.html" > < em > read_data< / em > < / a > or < a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / a > command
from a data or restart file.< / p >
< p > Hybrid models where dihedrals are computed using different dihedral
potentials can be setup using the < em > hybrid< / em > dihedral style.< / p >
< p > The coefficients associated with a dihedral style can be specified in
a data or restart file or via the < a class = "reference internal" href = "dihedral_coeff.html" > < em > dihedral_coeff< / em > < / a >
command.< / p >
< p > All dihedral potentials store their coefficient data in binary restart
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files which means dihedral_style and
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< a class = "reference internal" href = "dihedral_coeff.html" > < em > dihedral_coeff< / em > < / a > commands do not need to be
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re-specified in an input script that restarts a simulation. See the
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< a class = "reference internal" href = "read_restart.html" > < em > read_restart< / em > < / a > command for details on how to do
this. The one exception is that dihedral_style < em > hybrid< / em > only stores
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the list of sub-styles in the restart file; dihedral coefficients need
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to be re-specified.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > When both a dihedral and pair style is defined, the
< a class = "reference internal" href = "special_bonds.html" > < em > special_bonds< / em > < / a > command often needs to be used to
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turn off (or weight) the pairwise interaction that would otherwise
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exist between 4 bonded atoms.< / p >
< / div >
< p > In the formulas listed for each dihedral style, < em > phi< / em > is the torsional
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angle defined by the quadruplet of atoms. This angle has a sign
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convention as shown in this diagram:< / p >
< img alt = "_images/dihedral_sign.jpg" class = "align-center" src = "_images/dihedral_sign.jpg" / >
< p > where the I,J,K,L ordering of the 4 atoms that define the dihedral
is from left to right.< / p >
< p > This sign convention effects several of the dihedral styles listed
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below (e.g. charmm, helix) in the sense that the energy formula
depends on the sign of phi, which may be reflected in the value of the
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coefficients you specify.< / p >
< div class = "admonition warning" >
< p class = "first admonition-title" > Warning< / p >
< p class = "last" > When comparing the formulas and coefficients for
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various LAMMPS dihedral styles with dihedral equations defined by
other force fields, note that some force field implementations
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divide/multiply the energy prefactor < em > K< / em > by the multiple number of
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torsions that contain the J-K bond in an I-J-K-L torsion. LAMMPS does
not do this, i.e. the listed dihedral equation applies to each
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individual dihedral. Thus you need to define < em > K< / em > appropriately via
the < a class = "reference internal" href = "dihedral_coeff.html" > < em > dihedral_coeff< / em > < / a > command to account for this
difference if necessary.< / p >
< / div >
< hr class = "docutils" / >
< p > Here is an alphabetic list of dihedral styles defined in LAMMPS. Click on
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the style to display the formula it computes and coefficients
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specified by the associated < a class = "reference internal" href = "dihedral_coeff.html" > < em > dihedral_coeff< / em > < / a > command.< / p >
< p > Note that there are also additional dihedral styles submitted by users
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which are included in the LAMMPS distribution. The list of these with
links to the individual styles are given in the dihedral section of
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< a class = "reference internal" href = "Section_commands.html#cmd-5" > < span > this page< / span > < / a > .< / p >
< ul class = "simple" >
< li > < a class = "reference internal" href = "dihedral_none.html" > < em > dihedral_style none< / em > < / a > - turn off dihedral interactions< / li >
< li > < a class = "reference internal" href = "dihedral_hybrid.html" > < em > dihedral_style hybrid< / em > < / a > - define multiple styles of dihedral interactions< / li >
< li > < a class = "reference internal" href = "dihedral_charmm.html" > < em > dihedral_style charmm< / em > < / a > - CHARMM dihedral< / li >
< li > < a class = "reference internal" href = "dihedral_class2.html" > < em > dihedral_style class2< / em > < / a > - COMPASS (class 2) dihedral< / li >
< li > < a class = "reference internal" href = "dihedral_harmonic.html" > < em > dihedral_style harmonic< / em > < / a > - harmonic dihedral< / li >
< li > < a class = "reference internal" href = "dihedral_helix.html" > < em > dihedral_style helix< / em > < / a > - helix dihedral< / li >
< li > < a class = "reference internal" href = "dihedral_multi_harmonic.html" > < em > dihedral_style multi/harmonic< / em > < / a > - multi-harmonic dihedral< / li >
< li > < a class = "reference internal" href = "dihedral_opls.html" > < em > dihedral_style opls< / em > < / a > - OPLS dihedral< / li >
< / ul >
< / div >
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< div class = "section" id = "restrictions" >
< h2 > Restrictions< a class = "headerlink" href = "#restrictions" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > Dihedral styles can only be set for atom styles that allow dihedrals
to be defined.< / p >
< p > Most dihedral styles are part of the MOLECULE package. They are only
enabled if LAMMPS was built with that package. See the < a class = "reference internal" href = "Section_start.html#start-3" > < span > Making LAMMPS< / span > < / a > section for more info on packages.
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The doc pages for individual dihedral potentials tell if it is part of
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a package.< / p >
< / div >
< div class = "section" id = "related-commands" >
< h2 > Related commands< a class = "headerlink" href = "#related-commands" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > < a class = "reference internal" href = "dihedral_coeff.html" > < em > dihedral_coeff< / em > < / a > < / p >
< / div >
< div class = "section" id = "default" >
< h2 > Default< a class = "headerlink" href = "#default" title = "Permalink to this headline" > ¶< / a > < / h2 >
< p > dihedral_style none< / p >
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