253 lines
9.1 KiB
Plaintext
253 lines
9.1 KiB
Plaintext
.. index:: pair_style lj/charmm/coul/charmm
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pair_style lj/charmm/coul/charmm command
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========================================
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pair_style lj/charmm/coul/charmm/cuda command
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=============================================
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pair_style lj/charmm/coul/charmm/omp command
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============================================
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pair_style lj/charmm/coul/charmm/implicit command
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=================================================
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pair_style lj/charmm/coul/charmm/implicit/cuda command
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======================================================
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pair_style lj/charmm/coul/charmm/implicit/omp command
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=====================================================
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pair_style lj/charmm/coul/long command
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======================================
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pair_style lj/charmm/coul/long/cuda command
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===========================================
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pair_style lj/charmm/coul/long/gpu command
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==========================================
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pair_style lj/charmm/coul/long/intel command
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============================================
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pair_style lj/charmm/coul/long/opt command
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==========================================
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pair_style lj/charmm/coul/long/omp command
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==========================================
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pair_style lj/charmm/coul/msm command
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=====================================
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pair_style lj/charmm/coul/msm/omp command
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=========================================
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Syntax
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""""""
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.. parsed-literal::
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pair_style style args
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* style = *lj/charmm/coul/charmm* or *lj/charmm/coul/charmm/implicit* or *lj/charmm/coul/long* or *lj/charmm/coul/msm*
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* args = list of arguments for a particular style
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.. parsed-literal::
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*lj/charmm/coul/charmm* args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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*lj/charmm/coul/charmm/implicit* args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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*lj/charmm/coul/long* args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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*lj/charmm/coul/msm* args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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Examples
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""""""""
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.. parsed-literal::
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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.. parsed-literal::
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0
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pair_style lj/charmm/coul/charmm/implicit 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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.. parsed-literal::
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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.. parsed-literal::
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pair_style lj/charmm/coul/msm 8.0 10.0
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pair_style lj/charmm/coul/msm 8.0 10.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5
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Description
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"""""""""""
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The *lj/charmm* styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a widely
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used potential in the `CHARMM <http://www.scripps.edu/brooks>`_ MD code.
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See :ref:`(MacKerell) <pair-MacKerell>` for a description of the CHARMM force
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field.
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.. image:: Eqs/pair_charmm.jpg
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:align: center
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Both the LJ and Coulombic terms require an inner and outer cutoff.
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They can be the same for both formulas or different depending on
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whether 2 or 4 arguments are used in the pair_style command. In each
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case, the inner cutoff distance must be less than the outer cutoff.
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It it typical to make the difference between the 2 cutoffs about 1.0
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Angstrom.
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Style *lj/charmm/coul/charmm/implicit* computes the same formulas as
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style *lj/charmm/coul/charmm* except that an additional 1/r term is
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included in the Coulombic formula. The Coulombic energy thus varies
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as 1/r^2. This is effectively a distance-dependent dielectric term
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which is a simple model for an implicit solvent with additional
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screening. It is designed for use in a simulation of an unsolvated
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biomolecule (no explicit water molecules).
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Styles *lj/charmm/coul/long* and *lj/charmm/coul/msm* compute the same
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formulas as style *lj/charmm/coul/charmm* except that an additional
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damping factor is applied to the Coulombic term, as described for the
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:doc:`lj/cut <pair_lj>` pair styles. Only one Coulombic cutoff is
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specified for *lj/charmm/coul/long* and *lj/charmm/coul/msm*\ ; if only
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2 arguments are used in the pair_style command, then the outer LJ
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cutoff is used as the single Coulombic cutoff.
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The following coefficients must be defined for each pair of atoms
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types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
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above, or in the data file or restart files read by the
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:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
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commands, or by mixing as described below:
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* epsilon (energy units)
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* sigma (distance units)
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* epsilon_14 (energy units)
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* sigma_14 (distance units)
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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The latter 2 coefficients are optional. If they are specified, they
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are used in the LJ formula between 2 atoms of these types which are
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also first and fourth atoms in any dihedral. No cutoffs are specified
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because this CHARMM force field does not allow varying cutoffs for
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individual atom pairs; all pairs use the global cutoff(s) specified in
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the pair_style command.
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----------
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Styles with a *cuda*\ , *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in :doc:`Section_accelerate <Section_accelerate>`
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info.
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You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the :ref:`-suffix command-line switch <start_7>` when you invoke LAMMPS, or you can
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use the :doc:`suffix <suffix>` command in your input script.
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See :doc:`Section_accelerate <Section_accelerate>` of the manual for
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more instructions on how to use the accelerated styles effectively.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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For atom type pairs I,J and I != J, the epsilon, sigma, epsilon_14,
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and sigma_14 coefficients for all of the lj/charmm pair styles can be
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mixed. The default mix value is *arithmetic* to coincide with the
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usual settings for the CHARMM force field. See the "pair_modify"
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command for details.
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None of the lj/charmm pair styles support the
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:doc:`pair_modify <pair_modify>` shift option, since the Lennard-Jones
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portion of the pair interaction is smoothed to 0.0 at the cutoff.
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The *lj/charmm/coul/long* style supports the
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:doc:`pair_modify <pair_modify>` table option since it can tabulate the
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short-range portion of the long-range Coulombic interaction.
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None of the lj/charmm pair styles support the
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:doc:`pair_modify <pair_modify>` tail option for adding long-range tail
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corrections to energy and pressure, since the Lennard-Jones portion of
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the pair interaction is smoothed to 0.0 at the cutoff.
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All of the lj/charmm pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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The lj/charmm/coul/long pair style supports the use of the *inner*\ ,
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*middle*\ , and *outer* keywords of the :doc:`run_style respa <run_style>`
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command, meaning the pairwise forces can be partitioned by distance at
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different levels of the rRESPA hierarchy. The other styles only
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support the *pair* keyword of run_style respa. See the
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:doc:`run_style <run_style>` command for details.
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----------
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Restrictions
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""""""""""""
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The *lj/charmm/coul/charmm* and *lj/charmm/coul/charmm/implicit*
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styles are part of the MOLECULE package. The *lj/charmm/coul/long*
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style is part of the KSPACE package. They are only enabled if LAMMPS
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was built with those packages. See the :ref:`Making LAMMPS <start_3>` section for more info. Note that
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the MOLECULE and KSPACE packages are installed by default.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`
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**Default:** none
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----------
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.. _pair-MacKerell:
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**(MacKerell)** MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
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Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Section_commands.html#comm
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