2006-09-22 00:22:34 +08:00
|
|
|
<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>dihedral_style charmm command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>dihedral_style charmm
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>dihedral_style charmm
|
|
|
|
|
dihedral_coeff 1 120.0 1 60 0.5
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The <I>charmm</I> dihedral style uses the potential
|
|
|
|
|
</P>
|
|
|
|
|
<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
|
|
|
|
|
</CENTER>
|
2006-09-28 03:12:31 +08:00
|
|
|
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
|
2007-04-20 22:36:34 +08:00
|
|
|
field. This dihedral style can also be used for the AMBER force field
|
2007-12-01 07:36:27 +08:00
|
|
|
(see comment on weighting factors below). See <A HREF = "#Cornell">(Cornell)</A>
|
|
|
|
|
for a description of the AMBER force field.
|
2006-09-28 03:12:31 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
<P>The following coefficients must be defined for each dihedral type via the
|
|
|
|
|
<A HREF = "dihedral_coeff.html">dihedral_coeff</A> command as in the example above, or in
|
|
|
|
|
the data file or restart files read by the <A HREF = "read_data.html">read_data</A>
|
|
|
|
|
or <A HREF = "read_restart.html">read_restart</A> commands:
|
|
|
|
|
</P>
|
|
|
|
|
<UL><LI>K (energy)
|
|
|
|
|
<LI>n (integer >= 0)
|
|
|
|
|
<LI>d (integer value of degrees)
|
|
|
|
|
<LI>weighting factor (0.0 to 1.0)
|
|
|
|
|
</UL>
|
|
|
|
|
<P>The weighting factor is applied to pairwise interaction between the
|
2007-12-01 07:36:27 +08:00
|
|
|
1st and 4th atoms in the dihedral, which are computed by a CHARMM
|
|
|
|
|
<A HREF = "pair_charmm.html">pair_style</A> with epsilon and sigma values specified
|
|
|
|
|
with a <A HREF = "pair_charmm.html">pair_coeff</A> command. Note that this
|
|
|
|
|
weighting factor is unrelated to the weighting factor specified by the
|
|
|
|
|
<A HREF = "special_bonds.html">special bonds</A> command which applies to all 1-4
|
2007-04-20 22:36:34 +08:00
|
|
|
interactions in the system.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For CHARMM force fields, the special_bonds 1-4 weighting factor should
|
|
|
|
|
be set to 0.0. This is because the pair styles that contain "charmm"
|
|
|
|
|
(e.g. <A HREF = "pair_charmm.html">pair_style lj/charmm/coul/long</A>) define extra
|
|
|
|
|
1-4 interaction coefficients that are used by this dihedral style to
|
|
|
|
|
compute those interactions explicitly. This means that if any of the
|
|
|
|
|
weighting factors defined as dihedral coefficients (4th coeff above)
|
|
|
|
|
are non-zero, then you must use a charmm pair style. Note that if you
|
|
|
|
|
do not set the special_bonds 1-4 weighting factor to 0.0 (which is the
|
|
|
|
|
default) then 1-4 interactions in dihedrals will be computed twice,
|
|
|
|
|
once by the pair routine and once by the dihedral routine, which is
|
|
|
|
|
probably not what you want.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For AMBER force fields, the special_bonds 1-4 weighting factor should
|
|
|
|
|
be set to the AMBER defaults (1/2 and 5/6) and all the dihedral
|
|
|
|
|
weighting factors (4th coeff above) should be set to 0.0. In this
|
|
|
|
|
case, you can use any pair style you wish, since the dihedral does not
|
|
|
|
|
need any 1-4 information.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-06-25 22:36:36 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>This dihedral style can only be used if LAMMPS was built with the
|
|
|
|
|
"molecular" package (which it is by default). See the <A HREF = "Section_start.html#2_3">Making
|
|
|
|
|
LAMMPS</A> section for more info on packages.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B> none
|
|
|
|
|
</P>
|
2006-09-28 03:12:31 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2007-04-20 22:36:34 +08:00
|
|
|
<A NAME = "Cornell"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
|
|
|
|
|
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
|
|
|
|
|
</P>
|
2006-09-28 03:12:31 +08:00
|
|
|
<A NAME = "MacKerell"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
2008-02-08 08:09:12 +08:00
|
|
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
|
2006-09-28 03:12:31 +08:00
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
</HTML>
|
