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pair_hbond_dreiding.html
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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>
</CENTER>
<HR>
<H3>pair_style hbond/dreiding/lj command
</H3>
<H3>pair_style hbond/dreiding/lj/omp command
</H3>
<H3>pair_style hbond/dreiding/morse command
</H3>
<H3>pair_style hbond/dreiding/morse/omp command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof
</PRE>
<UL><LI>style = <I>hbond/dreiding/lj</I> or <I>hbond/dreiding/morse</I>
<LI>n = cosine angle periodicity
<LI>inner_distance_cutoff = global inner cutoff for Donor-Acceptor interactions (distance units)
<LI>outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
<LI>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
<LI>interactions (degrees)
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
</PRE>
<PRE>pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9 11 90
</PRE>
<P><B>Description:</B>
</P>
<P>The <I>hbond/dreiding</I> styles compute the Acceptor-Hydrogen-Donor (AHD)
3-body hydrogen bond interaction for the
<A HREF = "Section_howto.html#howto_4">DREIDING</A> force field, given by:
</P>
<CENTER><IMG SRC = "Eqs/pair_hbond_dreiding.jpg">
</CENTER>
<P>where Rin is the inner spline distance cutoff, Rout is the outer
distance cutoff, theta_c is the angle cutoff, and n is the cosine
periodicity.
</P>
<P>Here, <I>r</I> is the radial distance between the donor (D) and acceptor
(A) atoms and <I>theta</I> is the bond angle between the acceptor, the
hydrogen (H) and the donor atoms:
</P>
<CENTER><IMG SRC = "Eqs/dreiding_hbond.jpg">
</CENTER>
<P>These 3-body interactions can be defined for pairs of acceptor and
donor atoms, based on atom types. For each donor/acceptor atom pair,
the 3rd atom in the interaction is a hydrogen permanently bonded to
the donor atom, e.g. in a bond list read in from a data file via the
<A HREF = "read_data.html">read_data</A> command. The atom types of possible
hydrogen atoms for each donor/acceptor type pair are specified by the
<A HREF = "pair_coeff.html">pair_coeff</A> command (see below).
</P>
<P>Style <I>hbond/dreiding/lj</I> is the original DREIDING potential of
<A HREF = "#Mayo">(Mayo)</A>. It uses a LJ 12/10 functional for the Donor-Acceptor
interactions. To match the results in the original paper, use n = 4.
</P>
<P>Style <I>hbond/dreiding/morse</I> is an improved version using a Morse
potential for the Donor-Acceptor interactions. <A HREF = "#Liu">(Liu)</A> showed
that the Morse form gives improved results for Dendrimer simulations,
when n = 2.
</P>
<P>See this <A HREF = "Section_howto.html#howto_4">howto section</A> of the manual for
more information on the DREIDING forcefield.
</P>
<P>IMPORTANT NOTE: Because the Dreiding hydrogen bond potential is only
one portion of an overall force field which typically includes other
pairwise interactions, it is common to use it as a sub-style in a
<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> command, where another
pair style provides the repulsive core interaction between pairs of
atoms, e.g. a 1/r^12 Lennard-Jones repulsion.
</P>
<P>IMPORTANT NOTE: When using the hbond/dreiding pair styles with
<A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A>, you should explicitly
define pair interactions between the donor atom and acceptor atoms,
(as well as between these atoms and ALL other atoms in your system).
Whenever <A HREF = "pair_hybrid.html">pair_style hybrid/overlay</A> is used,
ordinary mixing rules are not applied to atoms like the donor and
acceptor atoms because they are typically referenced in multiple pair
styles. Neglecting to do this can cause difficult-to-detect physics
problems.
</P>
<P>IMPORTANT NOTE: In the original Dreiding force field paper 1-4
non-bonded interactions ARE allowed. If this is desired for your
model, use the special_bonds command (e.g. "special_bonds lj 0.0 0.0
1.0") to turn these interactions on.
</P>
<HR>
<P>The following coefficients must be defined for pairs of eligible
donor/acceptor types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as
in the examples above.
</P>
<P>IMPORTANT NOTE: Unlike other pair styles and their associated
<A HREF = "pair_coeff.html">pair_coeff</A> commands, you do not need to specify
pair_coeff settings for all possible I,J type pairs. Only I,J type
pairs for atoms which act as joint donors/acceptors need to be
specified; all other type pairs are assumed to be inactive.
</P>
<P>IMPORTANT NOTE: A <A HREF = "pair_coeff.html">pair_coeff</A> command can be
speficied multiple times for the same donor/acceptor type pair. This
enables multiple hydrogen types to be assigned to the same
donor/acceptor type pair. For other pair_styles, if the pair_coeff
command is re-used for the same I.J type pair, the settings for that
type pair are overwritten. For the hydrogen bond potentials this is
not the case; the settings are cummulative. This means the only way
to turn off a previous setting, is to re-use the pair_style command
and start over.
</P>
<P>For the <I>hbond/dreiding/lj</I> style the list of coefficients is as
follows:
</P>
<UL><LI>K = hydrogen atom type = 1 to Ntypes
<LI>donor flag = <I>i</I> or <I>j</I>
<LI>epsilon (energy units)
<LI>sigma (distance units)
<LI>n = exponent in formula above
<LI>distance cutoff Rin (distance units)
<LI>distance cutoff Rout (distance units)
<LI>angle cutoff (degrees)
</UL>
<P>For the <I>hbond/dreiding/morse</I> style the list of coefficients is as
follows:
</P>
<UL><LI>K = hydrogen atom type = 1 to Ntypes
<LI>donor flag = <I>i</I> or <I>j</I>
<LI>D0 (energy units)
<LI>alpha (1/distance units)
<LI>r0 (distance units)
<LI>n = exponent in formula above
<LI>distance cutoff Rin (distance units)
<LI>distance cutoff Rout (distance units)
<LI>angle cutoff (degrees)
</UL>
<P>A single hydrogen atom type K can be specified, or a wild-card
asterisk can be used in place of or in conjunction with the K
arguments to select multiple types as hydrogens. This takes the form
"*" or "*n" or "n*" or "m*n". See the <A HREF = "pair_coeff">pair_coeff</A> command
doc page for details.
</P>
<P>If the donor flag is <I>i</I>, then the atom of type I in the pair_coeff
command is treated as the donor, and J is the acceptor. If the donor
flag is <I>j</I>, then the atom of type J in the pair_coeff command is
treated as the donor and I is the donor. This option is required
because the <A HREF = "pair_coeff.html">pair_coeff</A> command requires that I <= J.
</P>
<P>Epsilon and sigma are settings for the hydrogen bond potential based
on a Lennard-Jones functional form. Note that sigma is defined as the
zero-crossing distance for the potential, not as the energy minimum at
2^(1/6) sigma.
</P>
<P>D0 and alpha and r0 are settings for the hydrogen bond potential based
on a Morse functional form.
</P>
<P>The last 3 coefficients for both styles are optional. If not
specified, the global n, distance cutoff, and angle cutoff specified
in the pair_style command are used. If you wish to only override the
2nd or 3rd optional parameter, you must also specify the preceding
optional parameters.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support mixing. You must explicitly identify
each donor/acceptor type pair.
</P>
<P>These styles do not support the <A HREF = "pair_modify.html">pair_modify</A> shift
option for the energy of the interactions.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
these pair styles.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
tail option for adding long-range tail corrections to energy and
pressure.
</P>
<P>These pair styles do not write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands need to be
re-specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<P>These pair styles tally a count of how many hydrogen bonding
interactions they calculate each timestep and the hbond energy. These
quantities can be accessed via the <A HREF = "compute_pair.html">compute pair</A>
command as a vector of values of length 2.
</P>
<P>To print these quantities to the log file (with a descriptive column
heading) the following commands could be included in an input script:
</P>
<PRE>compute hb all pair hbond/dreiding/lj
variable n_hbond equal c_hb[1] #number hbonds
variable E_hbond equal c_hb[2] #hbond energy
thermo_style custom step temp epair v_E_hbond
</PRE>
<HR>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Mayo"></A>
<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
</P>
<A NAME = "Liu"></A>
<P><B>(Liu)</B> Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
2798 (2009)
</P>
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