forked from lijiext/lammps
198 lines
9.0 KiB
Plaintext
198 lines
9.0 KiB
Plaintext
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
|
|
|
:link(lws,http://lammps.sandia.gov)
|
|
:link(ld,Manual.html)
|
|
:link(lc,Section_commands.html#comm)
|
|
|
|
:line
|
|
|
|
special_bonds command :h3
|
|
|
|
[Syntax:]
|
|
|
|
special_bonds keyword values ... :pre
|
|
|
|
one or more keyword/value pairs may be appended :ulb,l
|
|
keyword = {amber} or {charmm} or {dreiding} or {fene} or {lj/coul} or {lj} or {coul} or {angle} or {dihedral} or {extra} :l
|
|
{amber} values = none
|
|
{charmm} values = none
|
|
{dreiding} values = none
|
|
{fene} values = none
|
|
{lj/coul} values = w1,w2,w3
|
|
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
|
|
{lj} values = w1,w2,w3
|
|
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
|
|
{coul} values = w1,w2,w3
|
|
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
|
|
{angle} value = {yes} or {no}
|
|
{dihedral} value = {yes} or {no}
|
|
{extra} value = N
|
|
N = number of extra 1-2,1-3,1-4 interactions to save space for :pre
|
|
:ule
|
|
|
|
Examples:
|
|
|
|
special_bonds amber
|
|
special_bonds charmm
|
|
special_bonds fene dihedral no
|
|
special_bonds lj/coul 0.0 0.0 0.5 angle yes dihedral yes
|
|
special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 0.0 dihedral yes
|
|
special_bonds lj/coul 0 1 1 extra 2 :pre
|
|
|
|
[Description:]
|
|
|
|
Set weighting coefficients for pairwise energy and force contributions
|
|
from atom pairs that are permanently bonded to each other. These
|
|
weighting factors are used by all "pair styles"_pair_style.html in
|
|
LAMMPS that compute simple pairwise interactions. The Coulomb factors
|
|
are applied to any Coulomb (charge interaction) term that the
|
|
potential calculates. The LJ factors are applied to the remaining
|
|
terms that the potential calculates, whether they represent LJ
|
|
interactions or not. The weighting factors are a scaling pre-factor
|
|
on the energy and force between the pair of atoms. Permanent bonds
|
|
between atoms are specified by defining the bond topology in the data
|
|
file read by the "read_data"_read_data.html command and by using the
|
|
"bond_style"_bond_style.html command to define the bond potential.
|
|
|
|
IMPORTANT NOTE: These weighting factors are NOT used by "pair
|
|
styles"_pair_style.html that compute many-body interactions, since the
|
|
"bonds" that result from such interactions are not permanent, but are
|
|
created and broken dynamically as atom conformations change. Examples
|
|
of pair styles and potentials in this category are EAM, MEAM,
|
|
Stillinger-Weber, Tersoff, COMB, AIREBO, and ReaxFF. In fact, when
|
|
using these pair styles, it makes no sense to define permanent bonds
|
|
and to specify special_bonds weighting factors (unless they are
|
|
applied to a different part of the system via the "pair_style
|
|
hybrid"_pair_hybrid.html command). Though LAMMPS does not check for
|
|
this, using special_bonds with these potentials will result in errors
|
|
and possibly crash the code, because the definition of weighting
|
|
factors changes the format of the neighor list used by the pair
|
|
styles.
|
|
|
|
The 1st of the 3 coefficients (LJ or Coulombic) is the weighting
|
|
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
|
|
each other. The 2nd coefficient is the weighting factor on 1-3 atom
|
|
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
|
|
water molecule). The 3rd coefficient is the weighting factor on 1-4
|
|
atom pairs which are those separated by 3 bonds (e.g. the 1st and 4th
|
|
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
|
|
to 0.0, then the pairwise interaction is effectively turned off for
|
|
all pairs of atoms bonded to each other. If it is set to 1.0, then
|
|
that interaction will be at full strength.
|
|
|
|
IMPORTANT NOTE: For purposes of computing weighted pairwise
|
|
interactions, 1-3 and 1-4 interactions are not defined from the list
|
|
of angles or dihedrals used by the simulation. Rather, they are
|
|
inferred topologically from the set of bonds specified when the
|
|
simulation is defined from a data or restart file (see
|
|
"read_data"_read_data.html or "read_restart"_read_restart.html
|
|
commands). Thus the set of 1-2,1-3,1-4 interactions that the weights
|
|
apply to is the same whether angle and dihedral potentials are
|
|
computed or not, and remains the same even if bonds are constrained,
|
|
or turned off, or removed during a simulation.
|
|
|
|
The two exceptions to this rule are (a) if the {angle} or {dihedral}
|
|
keywords are set to {yes} (see below), or (b) if the
|
|
"delete_bonds"_delete_bonds.html command is used with the {special}
|
|
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
|
|
deleted; see the "delete_bonds"_delete_bonds.html command for more
|
|
details.
|
|
|
|
The {amber} keyword sets the 3 coefficients to 0.0, 0.0, 0.5 for LJ
|
|
interactions and to 0.0, 0.0, 0.8333 for Coulombic interactions, which
|
|
is the default for a commonly used version of the AMBER force field,
|
|
where the last value is really 5/6. See "(Cornell)"_#Cornell for a
|
|
description of the AMBER force field.
|
|
|
|
The {charmm} keyword sets the 3 coefficients to 0.0, 0.0, 0.0 for both
|
|
LJ and Coulombic interactions, which is the default for a commonly
|
|
used version of the CHARMM force field. Note that in pair styles
|
|
{lj/charmm/coul/charmm} and {lj/charmm/coul/long} the 1-4 coefficients
|
|
are defined explicitly, and these pairwise contributions are computed
|
|
as part of the charmm dihedral style - see the
|
|
"pair_coeff"_pair_coeff.html and "dihedral_style"_dihedral_style.html
|
|
commands for more information. See "(MacKerell)"_#MacKerell for a
|
|
description of the CHARMM force field.
|
|
|
|
The {dreiding} keyword sets the 3 coefficients to 0.0, 0.0, 1.0 for both
|
|
LJ and Coulombic interactions, which is the default for the Dreiding
|
|
force field, as discussed in "(Mayo)"_#Mayo.
|
|
|
|
The {fene} keyword sets the 3 coefficients to 0.0, 1.0, 1.0 for both
|
|
LJ and Coulombic interactions, which is consistent with a
|
|
coarse-grained polymer model with "FENE bonds"_bond_fene.html. See
|
|
"(Kremer)"_#Kremer for a description of FENE bonds.
|
|
|
|
The {lj/coul}, {lj}, and {coul} keywords allow the 3 coefficients to
|
|
be set explicitly. The {lj/coul} keyword sets both the LJ and
|
|
Coulombic coefficients to the same 3 values. The {lj} and {coul}
|
|
keywords only set either the LJ or Coulombic coefficients. Use both
|
|
of them if you wish to set the LJ coefficients to different values
|
|
than the Coulombic coefficients.
|
|
|
|
The {angle} keyword allows the 1-3 weighting factor to be ignored for
|
|
individual atom pairs if they are not listed as the first and last
|
|
atoms in any angle defined in the simulation or as 1,3 or 2,4 atoms in
|
|
any dihedral defined in the simulation. For example, imagine the 1-3
|
|
weighting factor is set to 0.5 and you have a linear molecule with 4
|
|
atoms and bonds as follows: 1-2-3-4. If your data file defines 1-2-3
|
|
as an angle, but does not define 2-3-4 as an angle or 1-2-3-4 as a
|
|
dihedral, then the pairwise interaction between atoms 1 and 3 will
|
|
always be weighted by 0.5, but different force fields use different
|
|
rules for weighting the pairwise interaction between atoms 2 and 4.
|
|
If the {angle} keyword is specified as {yes}, then the pairwise
|
|
interaction between atoms 2 and 4 will be unaffected (full weighting
|
|
of 1.0). If the {angle} keyword is specified as {no} which is the
|
|
default, then the 2,4 interaction will also be weighted by 0.5.
|
|
|
|
The {dihedral} keyword allows the 1-4 weighting factor to be ignored
|
|
for individual atom pairs if they are not listed as the first and last
|
|
atoms in any dihedral defined in the simulation. For example, imagine
|
|
the 1-4 weighting factor is set to 0.5 and you have a linear molecule
|
|
with 5 atoms and bonds as follows: 1-2-3-4-5. If your data file
|
|
defines 1-2-3-4 as a dihedral, but does not define 2-3-4-5 as a
|
|
dihedral, then the pairwise interaction between atoms 1 and 4 will
|
|
always be weighted by 0.5, but different force fields use different
|
|
rules for weighting the pairwise interaction between atoms 2 and 5.
|
|
If the {dihedral} keyword is specified as {yes}, then the pairwise
|
|
interaction between atoms 2 and 5 will be unaffected (full weighting
|
|
of 1.0). If the {dihedral} keyword is specified as {no} which is the
|
|
default, then the 2,5 interaction will also be weighted by 0.5.
|
|
|
|
The {extra} keyword is used when additional bonds will be created
|
|
during a simulation run, e.g. by the "fix
|
|
bond/create"_fix_bond_create.html command. A list of 1-2,1-3,1-4
|
|
neighbors for each atom is calculated and stored by LAMMPS. If new
|
|
bonds are created, the list needs to grow. Using the {extra} keyword
|
|
leaves empty space in the list for N additional bonds to be added. If
|
|
you do not do this, you may get an error when bonds are added.
|
|
|
|
[Restrictions:] none
|
|
|
|
[Related commands:]
|
|
|
|
"delete_bonds"_delete_bonds.html, "fix bond/create"_fix_bond_create.html
|
|
|
|
[Default:]
|
|
|
|
All 3 Lennard-Jones and 3 Coulobmic weighting coefficients = 0.0,
|
|
angle = no, dihedral = no, and extra = 0.
|
|
|
|
:line
|
|
|
|
:link(Cornell)
|
|
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
|
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
|
|
|
:link(Kremer)
|
|
[(Kremer)] Kremer, Grest, J Chem Phys, 92, 5057 (1990).
|
|
|
|
:link(MacKerell)
|
|
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
|
|
|
:link(Mayo)
|
|
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
|
|
(1990).
|
|
|