Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/special_bonds.html
25f93667ecc7lammm-master

Last Change
Raw File

special_bonds.html
View Options

<HTML>
<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>
</CENTER>
<HR>
<H3>special_bonds command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>special_bonds keyword values ...
</PRE>
<UL><LI>one or more keyword/value pairs may be appended
<LI>keyword = <I>amber</I> or <I>charmm</I> or <I>dreiding</I> or <I>fene</I> or <I>lj/coul</I> or <I>lj</I> or <I>coul</I> or <I>angle</I> or <I>dihedral</I> or <I>extra</I>
<PRE> <I>amber</I> values = none
<I>charmm</I> values = none
<I>dreiding</I> values = none
<I>fene</I> values = none
<I>lj/coul</I> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones and Coulombic interactions
<I>lj</I> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Lennard-Jones interactions
<I>coul</I> values = w1,w2,w3
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
<I>angle</I> value = <I>yes</I> or <I>no</I>
<I>dihedral</I> value = <I>yes</I> or <I>no</I>
<I>extra</I> value = N
N = number of extra 1-2,1-3,1-4 interactions to save space for
</PRE>
</UL>
<P>Examples:
</P>
<PRE>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>
<P><B>Description:</B>
</P>
<P>Set weighting coefficients for pairwise energy and force contributions
between pairs of atoms that are also permanently bonded to each other,
either directly or via one or two intermediate bonds. These weighting
factors are used by nearly all <A HREF = "pair_style.html">pair styles</A> in LAMMPS
that compute simple pairwise interactions. Permanent bonds between
atoms are specified by defining the bond topology in the data file
read by the <A HREF = "read_data.html">read_data</A> command. Typically a
<A HREF = "bond_style.html">bond_style</A> command is also used to define a bond
potential. The rationale for using these weighting factors is that
the interaction between a pair of bonded atoms is all (or mostly)
specified by the bond, angle, dihedral potentials, and thus the
non-bonded Lennard-Jones or Coulombic interaction between the pair of
atoms should be excluded (or reduced by a weighting factor).
</P>
<P>IMPORTANT NOTE: These weighting factors are NOT used by <A HREF = "pair_style.html">pair
styles</A> 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 in this category are EAM, MEAM, Stillinger-Weber,
Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
sense to define permanent bonds between atoms that interact via these
potentials, though such bonds may exist elsewhere in your system,
e.g. when using the <A HREF = "pair_hybrid.html">pair_style hybrid</A> command.
Thus LAMMPS ignores special_bonds settings when manybody potentials
are calculated.
</P>
<P>IMPORTANT NOTE: Unlike some commands in LAMMPS, you cannot use this
command multiple times in an incremental fashion: e.g. to first set
the LJ settings and then the Coulombic ones. Each time you use this
command it sets all the coefficients to default values and only
overrides the one you specify, so you should set all the options you
need each time you use it. See more details at the bottom of this
page.
</P>
<P>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. A value
of 1.0 means include the full interaction; a value of 0.0 means
exclude it completely.
</P>
<P>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.
</P>
<P>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
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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.
</P>
<P>The two exceptions to this rule are (a) if the <I>angle</I> or <I>dihedral</I>
keywords are set to <I>yes</I> (see below), or (b) if the
<A HREF = "delete_bonds.html">delete_bonds</A> command is used with the <I>special</I>
option that recomputes the 1-2,1-3,1-4 topologies after bonds are
deleted; see the <A HREF = "delete_bonds.html">delete_bonds</A> command for more
details.
</P>
<P>The <I>amber</I> 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 <A HREF = "#Cornell">(Cornell)</A> for a
description of the AMBER force field.
</P>
<P>The <I>charmm</I> 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
<I>lj/charmm/coul/charmm</I> and <I>lj/charmm/coul/long</I> the 1-4 coefficients
are defined explicitly, and these pairwise contributions are computed
as part of the charmm dihedral style - see the
<A HREF = "pair_coeff.html">pair_coeff</A> and <A HREF = "dihedral_style.html">dihedral_style</A>
commands for more information. See <A HREF = "#MacKerell">(MacKerell)</A> for a
description of the CHARMM force field.
</P>
<P>The <I>dreiding</I> 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 <A HREF = "#Mayo">(Mayo)</A>.
</P>
<P>The <I>fene</I> 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 <A HREF = "bond_fene.html">FENE bonds</A>. See
<A HREF = "#Kremer">(Kremer)</A> for a description of FENE bonds.
</P>
<P>The <I>lj/coul</I>, <I>lj</I>, and <I>coul</I> keywords allow the 3 coefficients to
be set explicitly. The <I>lj/coul</I> keyword sets both the LJ and
Coulombic coefficients to the same 3 values. The <I>lj</I> and <I>coul</I>
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.
</P>
<P>The <I>angle</I> 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 <I>angle</I> keyword is specified as <I>yes</I>, then the pairwise
interaction between atoms 2 and 4 will be unaffected (full weighting
of 1.0). If the <I>angle</I> keyword is specified as <I>no</I> which is the
default, then the 2,4 interaction will also be weighted by 0.5.
</P>
<P>The <I>dihedral</I> 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 <I>dihedral</I> keyword is specified as <I>yes</I>, then the pairwise
interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the <I>dihedral</I> keyword is specified as <I>no</I> which is the
default, then the 2,5 interaction will also be weighted by 0.5.
</P>
<P>The <I>extra</I> keyword can be used when additional bonds will be created
during a simulation run, e.g. by the <A HREF = "fix_bond_create.html">fix
bond/create</A> command. It can also be used if
molecules will be added to the system, e.g. via the <A HREF = "fix_deposit.html">fix
deposit</A>, or <A HREF = "fix_pour.html">fix pour</A> commands, which
will have atoms with more special neighbors than any atom in the
current system has.
</P>
<HR>
<P>IMPORTANT NOTE: LAMMPS stores and maintains a data structure with a
list of the 1st, 2nd, and 3rd neighbors of each atom (within the bond
topology of the system). If new bonds are created (or molecules added
containing atoms with more special neighbors), the size of this list
needs to grow. Note that adding a single bond always adds a new 1st
neighbor but may also induce *many* new 2nd and 3rd neighbors,
depending on the molecular topology of your system. Using the <I>extra</I>
keyword leaves empty space in the list for this N additional 1st, 2nd,
or 3rd neighbors to be added. If you do not do this, you may get an
error when bonds (or molecules) are added.
</P>
<HR>
<P>IMPORTANT NOTE: If you reuse this command in an input script, you
should set all the options you need each time. This command cannot be
used a 2nd time incrementally, e.g. to add some extra storage
locations via the <I>extra</I> keyword. E.g. these two commands:
</P>
<P>special_bonds lj 0.0 1.0 1.0
special_bonds coul 0.0 0.0 1.0
</P>
<P>are not the same as
</P>
<P>special_bonds lj 0.0 1.0 1.0 coul 0.0 0.0 1.0
</P>
<P>In the first case you end up with (after the 2nd command):
</P>
<P>LJ: 0.0 0.0 0.0
Coul: coul 0.0 0.0 1.0
</P>
<P>because the LJ settings are reset to their default values
each time the command is issued.
</P>
<P>Likewise
</P>
<PRE>special_bonds amber
special_bonds extra 2
</PRE>
<P>is not the same as this single command:
</P>
<PRE>special_bonds amber extra 2
</PRE>
<P>since in the former case, the 2nd command will reset all the LJ and
Coulombic weights to 0.0 (the default).
</P>
<P>One exception to this rule is the <I>extra</I> option itself. It is not
reset to its default value of 0 each time the special_bonds command is
invoked. This is because it can also be set by the
<A HREF = "read_data.html">read_data</A> and <A HREF = "create_box.html">create_box</A> commands,
so this command will not override those settings unless you explicitly
use <I>extra</I> as an option.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "delete_bonds.html">delete_bonds</A>, <A HREF = "fix_bond_create.html">fix bond/create</A>
</P>
<P><B>Default:</B>
</P>
<P>All 3 Lennard-Jones and 3 Coulombic weighting coefficients = 0.0,
angle = no, dihedral = no, and extra = 0.
</P>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "Kremer"></A>
<P><B>(Kremer)</B> Kremer, Grest, J Chem Phys, 92, 5057 (1990).
</P>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
</P>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
</HTML>
c4science · Help