git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5130 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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206
doc/pair_hbond_dreiding.html
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206
doc/pair_hbond_dreiding.html
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<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>
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</CENTER>
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<HR>
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<H3>pair_style hbond/dreiding/lj command
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</H3>
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<H3>pair_style hbond/dreiding/morse command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>pair_style style distance_cutoff angle_cutof N
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</PRE>
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<UL><LI>style = <I>hbond/dreiding/lj</I> or <I>hbond/dreiding/morse</I>
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<LI>n = cosine angle periodicity
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<LI>distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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<LI>angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
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<LI>interactions (degrees)
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style hbond/dreiding/lj 4 5.0 90
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pair_coeff * * 100.0 1.5 200.0
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pair_coeff * * 100.0 1.5 200.0 2
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</PRE>
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<PRE>pair_style hbond/dreiding/morse 2 4.6 75.0
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pair_coeff * * 100.0 1.5 200.0
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pair_coeff * * 100.0 1.5 200.0 4 3.0
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>The <I>hbond/dreiding</I> styles compute the Acceptor-Hydrogen-Donor (AHD)
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3-body hydrogen bond interaction for the
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<A HREF = "Section_howto.html#4_4">DREIDING</A> force field, given by:
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</P>
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<CENTER><IMG SRC = "Eqs/pair_hbond_dreiding.jpg">
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</CENTER>
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<P>where Rc is the distance cutoff, theta_c is the angle cutoff, and n is
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the cosine periodicity.
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</P>
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<P>Here, <I>r</I> is the radial distance between the donor (D) and acceptor
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(A) atoms and <I>theta</I> is the bond angle between the acceptor, the
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hydrogen (H) and the donor atoms:
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</P>
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<CENTER><IMG SRC = "Eqs/dreiding_hbond.jpg">
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</CENTER>
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<P>These 3-body interactions can be defined for pairs of acceptor and
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donor atoms, based on atom types. For each donor/acceptor atom pair,
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the 3rd atom in the interaction is a hydrogen permanently bonded to
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the donor atom, e.g. in a bond list read in from a data file via the
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<A HREF = "read_data.html">read_data</A> command. The atom types of possible
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hydrogen atoms for each donor/acceptor type pair are specified by the
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<A HREF = "pair_coeff.html">pair_coeff</A> command (see below).
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</P>
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<P>Style <I>hbond/dreiding/lj</I> is the original DREIDING potential of
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<A HREF = "#Mayo">(Mayo)</A>. It uses a LJ 12/10 functional for the Donor-Acceptor
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interactions. To match the results in the original paper, use n = 4.
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</P>
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<P>Style <I>hbond/dreiding/morse</I> is an improved version using a Morse
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potential for the Donor-Acceptor interactions. <A HREF = "#Liu">(Liu)</A> showed
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that the Morse form gives improved results for Dendrimer simulations,
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when n = 2.
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</P>
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<P>See this <A HREF = "Section_howto.html#4_4">howto section</A> of the manual for more
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information on the DREIDING forcefield.
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</P>
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<P>Because the Dreiding hydrogen bond potential is only one portion of
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an overall force field which typically includes other pairwise
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interactions, it is common to use it as a sub-style in a <A HREF = "pair_hybrid.html">pair_style
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hybrid or hybrid/overlay</A> command.
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</P>
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<P>The following coefficients must be defined for pairs of eligible
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donor/acceptor types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as
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in the examples above.
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</P>
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<P>IMPORTANT NOTE: Unlike other pair styles and their associated
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<A HREF = "pair_coeff.html">pair_coeff</A> commands, you do not need to specify
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pair_coeff settings for all possible I,J type pairs. Only I,J type
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pairs for atoms which act as joint donors/acceptors need to be
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specified; all other type pairs are assumed to be inactive.
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</P>
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<P>IMPORTANT NOTE: A <A HREF = "pair_coeff.html">pair_coeff</A> command can be
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speficied multiple times for the same donor/acceptor type pair. This
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enables multiple hydrogen types to be assigned to the same
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donor/acceptor type pair. For other pair_styles, if the pair_coeff
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command is re-used for the same I.J type pair, the settings for that
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type pair are overwritten. For the hydrogen bond potentials this is
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not the case; the settings are cummulative. This means the only way
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to turn off a previous setting, is to re-use the pair_style command
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and start over.
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</P>
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<P>For the <I>hbond/dreiding/lj</I> style the list of coefficients is as
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follows:
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</P>
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<UL><LI>K = hydrogen atom type = 1 to Ntypes
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<LI>donor flag = <I>i</I> or <I>j</I>
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<LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>n = exponent in formula above
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<LI>distance cutoff (distance units)
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<LI>angle cutoff (degrees)
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</UL>
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<P>For the <I>hbond/dreiding/morse</I> style the list of coefficients is as
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follows:
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</P>
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<UL><LI>K = hydrogen atom type = 1 to Ntypes
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<LI>donor flag = <I>i</I> or <I>j</I>
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<LI>D0 (energy units)
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<LI>alpha (1/distance units)
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<LI>r0 (distance units)
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<LI>n = exponent in formula above
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<LI>distance cutoff (distance units)
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<LI>angle cutoff (degrees)
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</UL>
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<P>A single hydrogen atom type K can be specified, or a wild-card
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asterisk can be used in place of or in conjunction with the K
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arguments to select multiple types as hydrogens. This takes the form
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"*" or "*n" or "n*" or "m*n". See the <A HREF = "pair_coeff">pair_coeff</A> command
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doc page for details.
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</P>
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<P>If the donor flag is <I>i</I>, then the atom of type I in the pair_coeff
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command is treated as the donor, and J is the acceptor. If the donor
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flag is <I>j</I>, then the atom of type J in the pair_coeff command is
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treated as the donor and I is the donor. This option is required
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because the <A HREF = "pair_coeff.html">pair_coeff</A> command requires that I <= J.
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</P>
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<P>Epsilon and sigma are settings for the hydrogen bond potential based
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on a Lennard-Jones functional form. Note that sigma is defined as the
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zero-crossing distance for the potential, not as the energy minimum at
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2^(1/6) sigma.
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</P>
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<P>D0 and alpha and r0 are settings for the hydrogen bond potential based
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on a Morse functional form.
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</P>
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<P>The last 3 coefficients for both styles are optional. If not
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specified, the global n, distance cutoff, and angle cutoff specified
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in the pair_style command are used. If you wish to only override the
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2nd or 3rd optional parameter, you must also specify the preceding
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optional parameters.
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</P>
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<HR>
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<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
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</P>
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<P>These pair styles do not support mixing. You must explicitly identify
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each donor/acceptor type pair.
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</P>
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<P>These styles do not support the <A HREF = "pair_modify.html">pair_modify</A> shift
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option for the energy of the interactions.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant for
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these pair styles.
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</P>
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<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
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tail option for adding long-range tail corrections to energy and
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pressure.
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</P>
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<P>These pair styles do not write their information to <A HREF = "restart.html">binary restart
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files</A>, so pair_style and pair_coeff commands need to be
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re-specified in an input script that reads a restart file.
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</P>
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<P>These pair styles can only be used via the <I>pair</I> keyword of the
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<A HREF = "run_style.html">run_style respa</A> command. They do not support the
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<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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<P>These pair style tally a count of how many hydrogen bonding
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interactions they calculate each timestep. This quantity can be
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accessed via the <A HREF = "compute_pair.html">compute pair</A> command as a vector
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of values of length 1.
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</P>
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<P>To print this quantity to the log file (with a descriptive column
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||||
heading) the following commands could be included in an input script:
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</P>
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<PRE>compute hb all pair hbond/dreiding/lj
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variable hb equal c_hb[1]
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thermo_style custom step temp epair v_hb
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</PRE>
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<HR>
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<P><B>Restrictions:</B> none
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "pair_coeff.html">pair_coeff</A>
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Mayo"></A>
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<P><B>(Mayo)</B> Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
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(1990).
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</P>
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<A NAME = "Liu"></A>
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<P><B>(Liu)</B> Liu, Bryantsev, Diallo, Goddard III, J. Am. Chem. Soc 131 (8)
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2798 (2009)
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</P>
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</HTML>
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198
doc/pair_hbond_dreiding.txt
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198
doc/pair_hbond_dreiding.txt
Normal file
@ -0,0 +1,198 @@
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"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
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:link(lws,http://lammps.sandia.gov)
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:link(ld,Manual.html)
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:link(lc,Section_commands.html#comm)
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:line
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pair_style hbond/dreiding/lj command :h3
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pair_style hbond/dreiding/morse command :h3
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[Syntax:]
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pair_style style distance_cutoff angle_cutof N :pre
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style = {hbond/dreiding/lj} or {hbond/dreiding/morse}
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n = cosine angle periodicity
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distance_cutoff = global cutoff for Donor-Acceptor interactions (distance units)
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||||
angle_cutoff = global angle cutoff for Acceptor-Hydrogen-Donor
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interactions (degrees) :ul
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||||
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||||
[Examples:]
|
||||
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||||
pair_style hbond/dreiding/lj 4 5.0 90
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pair_coeff * * 100.0 1.5 200.0
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||||
pair_coeff * * 100.0 1.5 200.0 2 :pre
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||||
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||||
pair_style hbond/dreiding/morse 2 4.6 75.0
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pair_coeff * * 100.0 1.5 200.0
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pair_coeff * * 100.0 1.5 200.0 4 3.0 :pre
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||||
[Description:]
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||||
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The {hbond/dreiding} styles compute the Acceptor-Hydrogen-Donor (AHD)
|
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3-body hydrogen bond interaction for the
|
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"DREIDING"_Section_howto.html#4_4 force field, given by:
|
||||
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:c,image(Eqs/pair_hbond_dreiding.jpg)
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||||
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||||
where Rc is the distance cutoff, theta_c is the angle cutoff, and n is
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||||
the cosine periodicity.
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||||
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Here, {r} is the radial distance between the donor (D) and acceptor
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(A) atoms and {theta} is the bond angle between the acceptor, the
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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#4_4 of the manual for more
|
||||
information on the DREIDING forcefield.
|
||||
|
||||
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 or hybrid/overlay"_pair_hybrid.html command.
|
||||
|
||||
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 (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 (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
|
||||
|
||||
[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 style tally a count of how many hydrogen bonding
|
||||
interactions they calculate each timestep. This quantity can be
|
||||
accessed via the "compute pair"_compute_pair.html command as a vector
|
||||
of values of length 1.
|
||||
|
||||
To print this quantity 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 hb equal c_hb\[1\]
|
||||
thermo_style custom step temp epair v_hb :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)
|
||||
Reference in New Issue
Block a user