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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 lj/gromacs command
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</H3>
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<H3>pair_style lj/gromacs/coul/gromacs 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 args
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</PRE>
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<UL><LI>style = <I>lj/gromacs</I> or <I>lj/gromacs/coul/gromacs</I>
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<LI>args = list of arguments for a particular style
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</UL>
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<PRE> <I>lj/gromacs</I> args = inner outer
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inner, outer = global switching cutoffs for Lennard Jones
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<I>lj/gromacs/coul/gromacs</I> args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional)
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</PRE>
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<P><B>Examples:</B>
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</P>
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<PRE>pair_style lj/gromacs 9.0 12.0
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pair_coeff * * 100.0 2.0
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pair_coeff 2 2 100.0 2.0 8.0 10.0
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</PRE>
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<PRE>pair_style lj/gromacs/coul/gromacs 9.0 12.0
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pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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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>lj/gromacs</I> styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a commonly
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used potential in the <A HREF = "http://www.gromacs.org">GROMACS</A> MD code and for
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the coarse-grained models of "(Marrink")_#Marrink.
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</P>
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<CENTER><IMG SRC = "Eqs/pair_gromacs.jpg">
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</CENTER>
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<P>R1 is the inner cutoff; Rc is the outer cutoff. The coefficients A
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and B are computed by LAMMPS to perform the smoothing. The function
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S(r) is actually applied once to each term of the LJ formula and once
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to the Coulombic formula, so there are 2 or 3 sets of A,B coefficients
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depending on which pair_style is used. The boundary conditions
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applied to the smoothing function are as follows: S(r1) = S'(r1) = 0,
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S(rc) = -F(rc), S'(rc) = -F'(rc), where F(r) is the correpsonding term
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in the LJ or Coulombic function and a single quote represents a
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derivative with respect to r.
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</P>
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<P>The inner and outer cutoff for the LJ and Coulombic terms can be the
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same or different depending on whether 2 or 4 arguments are used in
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the pair_style command. The inner LJ cutoff must be > 0, but the
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inner Coulombic cutoff can be >= 0.
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</P>
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<P>The following coefficients must be defined for each pair of atoms
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types via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples
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above, or in the data file or restart files read by the
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<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
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commands, or by mixing as described below:
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</P>
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<UL><LI>epsilon (energy units)
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<LI>sigma (distance units)
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<LI>inner (distance units)
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<LI>outer (distance units)
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</UL>
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<P>Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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</P>
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<P>The last 2 coefficients are optional inner and outer cutoffs for style
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<I>lj/gromacs</I>. If not specified, the global <I>inner</I> and <I>outer</I> values
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are used.
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</P>
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<P>The last 2 coefficients cannot be used with style
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<I>lj/gromacs/coul/gromacs</I> because this force field does not allow
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varying cutoffs for individual atom pairs; all pairs use the global
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cutoff(s) specified in the pair_style command.
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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>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/cut pair styles can be mixed.
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The default mix value is <I>geometric</I>. See the "pair_modify" command
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for details.
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</P>
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<P>None of the GROMACS pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> shift option, since the Lennard-Jones
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portion of the pair interaction is already smoothed to 0.0 at the
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cutoff.
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</P>
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<P>The <A HREF = "pair_modify.html">pair_modify</A> table option is not relevant
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for this pair style.
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</P>
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<P>None of the GROMACS pair styles support the
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<A HREF = "pair_modify.html">pair_modify</A> tail option for adding long-range tail
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corrections to energy and pressure, since there are no corrections for
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a potential that goes to 0.0 at the cutoff.
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</P>
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<P>All of the GROMACS pair styles write their information to <A HREF = "restart.html">binary
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restart files</A>, so pair_style and pair_coeff commands do
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not need to be specified in an input script that reads a restart file.
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</P>
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<P>All of the GROMACS pair styles can only be used via the <I>pair</I>
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keyword of the <A HREF = "run_style.html">run_style respa</A> command. They do not
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support the <I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
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</P>
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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 = "Marrink"></A>
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<P><B>(Marrink)</B> Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
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</P>
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</HTML>
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@ -0,0 +1,126 @@
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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 lj/gromacs command :h3
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pair_style lj/gromacs/coul/gromacs command :h3
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[Syntax:]
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pair_style style args :pre
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style = {lj/gromacs} or {lj/gromacs/coul/gromacs}
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args = list of arguments for a particular style :ul
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{lj/gromacs} args = inner outer
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inner, outer = global switching cutoffs for Lennard Jones
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{lj/gromacs/coul/gromacs} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner2, outer2 = global switching cutoffs for Coulombic (optional) :pre
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[Examples:]
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pair_style lj/gromacs 9.0 12.0
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pair_coeff * * 100.0 2.0
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pair_coeff 2 2 100.0 2.0 8.0 10.0 :pre
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pair_style lj/gromacs/coul/gromacs 9.0 12.0
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pair_style lj/gromacs/coul/gromacs 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0 :pre
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[Description:]
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The {lj/gromacs} styles compute LJ and Coulombic interactions with an
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additional switching function S(r) that ramps the energy and force
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smoothly to zero between an inner and outer cutoff. It is a commonly
|
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used potential in the "GROMACS"_http://www.gromacs.org MD code and for
|
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the coarse-grained models of "(Marrink")_#Marrink.
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:c,image(Eqs/pair_gromacs.jpg)
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R1 is the inner cutoff; Rc is the outer cutoff. The coefficients A
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and B are computed by LAMMPS to perform the smoothing. The function
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S(r) is actually applied once to each term of the LJ formula and once
|
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to the Coulombic formula, so there are 2 or 3 sets of A,B coefficients
|
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depending on which pair_style is used. The boundary conditions
|
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applied to the smoothing function are as follows: S(r1) = S'(r1) = 0,
|
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S(rc) = -F(rc), S'(rc) = -F'(rc), where F(r) is the correpsonding term
|
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in the LJ or Coulombic function and a single quote represents a
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derivative with respect to r.
|
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The inner and outer cutoff for the LJ and Coulombic terms can be the
|
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same or different depending on whether 2 or 4 arguments are used in
|
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the pair_style command. The inner LJ cutoff must be > 0, but the
|
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inner Coulombic cutoff can be >= 0.
|
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|
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The following coefficients must be defined for each pair of atoms
|
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types via the "pair_coeff"_pair_coeff.html command as in the examples
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above, or in the data file or restart files read by the
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"read_data"_read_data.html or "read_restart"_read_restart.html
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commands, or by mixing as described below:
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epsilon (energy units)
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sigma (distance units)
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inner (distance units)
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outer (distance units) :ul
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Note that sigma is defined in the LJ formula as the zero-crossing
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distance for the potential, not as the energy minimum at 2^(1/6)
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sigma.
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The last 2 coefficients are optional inner and outer cutoffs for style
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{lj/gromacs}. If not specified, the global {inner} and {outer} values
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are used.
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The last 2 coefficients cannot be used with style
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{lj/gromacs/coul/gromacs} because this force field does not allow
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varying cutoffs for individual atom pairs; all pairs use the global
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cutoff(s) specified in the pair_style command.
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:line
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[Mixing, shift, table, tail correction, restart, rRESPA info]:
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|
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For atom type pairs I,J and I != J, the epsilon and sigma coefficients
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and cutoff distance for all of the lj/cut pair styles can be mixed.
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The default mix value is {geometric}. See the "pair_modify" command
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for details.
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None of the GROMACS pair styles support the
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"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
|
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portion of the pair interaction is already smoothed to 0.0 at the
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cutoff.
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The "pair_modify"_pair_modify.html table option is not relevant
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for this pair style.
|
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None of the GROMACS pair styles support the
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"pair_modify"_pair_modify.html tail option for adding long-range tail
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corrections to energy and pressure, since there are no corrections for
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a potential that goes to 0.0 at the cutoff.
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|
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All of the GROMACS pair styles write their information to "binary
|
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restart files"_restart.html, so pair_style and pair_coeff commands do
|
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not need to be specified in an input script that reads a restart file.
|
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|
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All of the GROMACS pair styles can only be used via the {pair}
|
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keyword of the "run_style respa"_run_style.html command. They do not
|
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support the {inner}, {middle}, {outer} keywords.
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:line
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[Restrictions:] none
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[Related commands:]
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"pair_coeff"_pair_coeff.html
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[Default:] none
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:line
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:link(Marrink)
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[(Marrink)] Marrink, de Vries, Mark, J Phys Chem B, 108, 750-760 (2004).
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