Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/doc2/dihedral_charmm.html
c7d0f4d9f2delammm-master-deprecated

Last Change
Raw File

dihedral_charmm.html
View Options

<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>
<H3>dihedral_style charmm/kk command
</H3>
<H3>dihedral_style charmm/omp 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>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field. This dihedral style can also be used for the AMBER force field
(see comment on weighting factors below). See <A HREF = "#Cornell">(Cornell)</A>
for a description of the AMBER force field.
</P>
<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
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
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.
</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>Restrictions:</B>
</P>
<P>This dihedral style can only be used if LAMMPS was built with the
MOLECULE package (which it is by default). See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info on packages.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "dihedral_coeff.html">dihedral_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Cornell"></A>
<P><B>(Cornell)</B> Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
</P>
<A NAME = "MacKerell"></A>
<P><B>(MacKerell)</B> MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem B, 102, 3586 (1998).
</P>
</HTML>
c4science · Help