Homec4science
Diffusion lammps (lammm-master) Browse

lammps/doc/pair_hbond_dreiding.txt
427161ef56aalammm-master

Last Change
Raw File

pair_hbond_dreiding.txt
View Options

"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
pair_style hbond/dreiding/lj command :h3
pair_style hbond/dreiding/lj/omp command :h3
pair_style hbond/dreiding/morse command :h3
pair_style hbond/dreiding/morse/omp command :h3
[Syntax:]
pair_style style N inner_distance_cutoff outer_distance_cutoff angle_cutof :pre
style = {hbond/dreiding/lj} or {hbond/dreiding/morse}
n = cosine angle periodicity
inner_distance_cutoff = global inner spline cutoff for Donor-Acceptor interactions (distance units)
outer_distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
interactions (degrees) :ul
[Examples:]
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
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
[Description:]
The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
3-body hydrogen bond interaction for the
"DREIDING"_Section_howto.html#howto_4 force field, given by:
:c,image(Eqs/pair_hbond_dreiding.jpg)
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.
Here, {r} is the radial distance between the donor (D) and acceptor
(A) atoms and {theta} is the bond angle between the acceptor, the
hydrogen (H) and the donor atoms:
:c,image(Eqs/dreiding_hbond.jpg)
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
"read_data"_read_data.html command. The atom types of possible
hydrogen atoms for each donor/acceptor type pair are specified by the
"pair_coeff"_pair_coeff.html command (see below).
Style {hbond/dreiding/lj} is the original DREIDING potential of
"(Mayo)"_#Mayo. It uses a LJ 12/10 functional for the Donor-Acceptor
interactions. To match the results in the original paper, use n = 4.
Style {hbond/dreiding/morse} is an improved version using a Morse
potential for the Donor-Acceptor interactions. "(Liu)"_#Liu showed
that the Morse form gives improved results for Dendrimer simulations,
when n = 2.
See this "howto section"_Section_howto.html#howto_4 of the manual for
more information on the DREIDING forcefield.
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
"pair_style hybrid/overlay"_pair_hybrid.html command, where another
pair style provides the repulsive core interaction between pairs of
atoms, e.g. a 1/r^12 Lennard-Jones repulsion.
IMPORTANT NOTE: When using the hbond/dreiding pair styles with
"pair_style hybrid/overlay"_pair_hybrid.html, 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 "pair_style hybrid/overlay"_pair_hybrid.html 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.
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.
:line
The following coefficients must be defined for pairs of eligible
donor/acceptor types via the "pair_coeff"_pair_coeff.html command as
in the examples above.
IMPORTANT NOTE: Unlike other pair styles and their associated
"pair_coeff"_pair_coeff.html 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.
IMPORTANT NOTE: A "pair_coeff"_pair_coeff.html 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.
For the {hbond/dreiding/lj} style the list of coefficients is as
follows:
K = hydrogen atom type = 1 to Ntypes
donor flag = {i} or {j}
epsilon (energy units)
sigma (distance units)
n = exponent in formula above
distance cutoff Rin (distance units)
distance cutoff Rout (distance units)
angle cutoff (degrees) :ul
For the {hbond/dreiding/morse} style the list of coefficients is as
follows:
K = hydrogen atom type = 1 to Ntypes
donor flag = {i} or {j}
D0 (energy units)
alpha (1/distance units)
r0 (distance units)
n = exponent in formula above
distance cutoff Rin (distance units)
distance cutoff Rout (distance units)
angle cutoff (degrees) :ul
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 "pair_coeff"_pair_coeff command
doc page for details.
If the donor flag is {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 {j}, 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 "pair_coeff"_pair_coeff.html command requires that I <= J.
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.
D0 and alpha and r0 are settings for the hydrogen bond potential based
on a Morse functional form.
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.
:line
Styles with a {cuda}, {gpu}, {omp}, or {opt} 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 "Section_accelerate"_Section_accelerate.html of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
These pair styles do not support mixing. You must explicitly identify
each donor/acceptor type pair.
These styles do not support the "pair_modify"_pair_modify.html shift
option for the energy of the interactions.
The "pair_modify"_pair_modify.html table option is not relevant for
these pair styles.
These pair styles do not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections to energy and
pressure.
These pair styles do not write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands need to be
re-specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
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 "compute pair"_compute_pair.html
command as a vector of values of length 2.
To print these quantities to the log file (with a descriptive column
heading) the following commands could be included in an input script:
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
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Mayo)
[(Mayo)] Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
(1990).
:link(Liu)
[(Liu)] Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
2798 (2009)
c4science · Help