From 4db2ef4ec6684010e7bf250b1978b22e704b8ee7 Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 20 Apr 2007 14:36:34 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@501 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/dihedral_charmm.html | 32 +++++++++++++++++++++++++++----- doc/dihedral_charmm.txt | 31 ++++++++++++++++++++++++++----- 2 files changed, 53 insertions(+), 10 deletions(-) diff --git a/doc/dihedral_charmm.html b/doc/dihedral_charmm.html index 2dc5e0c258..5e3ad0f845 100644 --- a/doc/dihedral_charmm.html +++ b/doc/dihedral_charmm.html @@ -27,7 +27,9 @@ dihedral_coeff 1 120.0 1 60 0.5

See (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) for a description of the AMBER force field.

The following coefficients must be defined for each dihedral type via the dihedral_coeff command as in the example above, or in @@ -43,10 +45,25 @@ or read_restart commands: 1st and 4th atoms in the dihedral. Note that this weighting factor is unrelated to the weighting factor specified by the special bonds 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) 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

@@ -58,6 +75,11 @@ by the dihedral/charmm potential).

+ + +

(Cornell) Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, +Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995). +

(MacKerell) MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field, diff --git a/doc/dihedral_charmm.txt b/doc/dihedral_charmm.txt index 788bd79ce2..62e6c24e4f 100644 --- a/doc/dihedral_charmm.txt +++ b/doc/dihedral_charmm.txt @@ -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).