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sjplimp 2007-04-20 14:36:34 +00:00
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commit 4db2ef4ec6
2 changed files with 53 additions and 10 deletions

32
doc/dihedral_charmm.html
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@ -27,7 +27,9 @@ dihedral_coeff 1 120.0 1 60 0.5
<CENTER><IMG SRC = "Eqs/dihedral_charmm.jpg">
</CENTER>
<P>See <A HREF = "#MacKerell">(MacKerell)</A> for a description of the CHARMM force
field.
field. This dihedral style can also be used for the AMBER force field
(see the 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
@ -43,10 +45,25 @@ or <A HREF = "read_restart.html">read_restart</A> commands:
1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the <A HREF = "doc/special_bonds.html">special
bonds</A> command which applies to all 1-4
interactions in the system. For CHARMM force fields, the latter
should typically be set to 0.0, else the 1-4 interactions in a
dihedral will be computed twice (once by the pair potential, and once
by the dihedral/charmm potential).
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>
<P><B>Restrictions:</B> none
</P>
@ -58,6 +75,11 @@ by the dihedral/charmm potential).
</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,

31
doc/dihedral_charmm.txt
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@ -24,7 +24,9 @@ The {charmm} dihedral style uses the potential
:c,image(Eqs/dihedral_charmm.jpg)
See "(MacKerell)"_#MacKerell for a description of the CHARMM force
field.
field. This dihedral style can also be used for the AMBER force field
(see the comment on weighting factors below). See
"(Cornell)"_#Cornell for a description of the AMBER force field.
The following coefficients must be defined for each dihedral type via the
"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
@ -40,10 +42,25 @@ The weighting factor is applied to pairwise interaction between the
1st and 4th atoms in the dihedral. Note that this weighting factor is
unrelated to the weighting factor specified by the "special
bonds"_doc/special_bonds.html command which applies to all 1-4
interactions in the system. For CHARMM force fields, the latter
should typically be set to 0.0, else the 1-4 interactions in a
dihedral will be computed twice (once by the pair potential, and once
by the dihedral/charmm potential).
interactions in the system.
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. "pair_style lj/charmm/coul/long"_pair_charmm.html) 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.
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.
[Restrictions:] none
@ -55,6 +72,10 @@ by the dihedral/charmm potential).
:line
:link(Cornell)
[(Cornell)] Cornell, Cieplak, Bayly, Gould, Merz, Ferguson,
Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
:link(MacKerell)
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).