From c936d176fc9bea328b097d73e13aeb153a207d4f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 25 Oct 2010 20:30:15 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5131 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/Section_commands.html | 26 +++---- doc/Section_commands.txt | 6 +- doc/Section_howto.html | 160 +++++++++++++++----------------------- doc/Section_howto.txt | 156 ++++++++++++++----------------------- doc/compute_pair.html | 62 +++++++++------ doc/compute_pair.txt | 62 +++++++++------ doc/special_bonds.html | 37 ++++++++- doc/special_bonds.txt | 34 +++++++- 8 files changed, 280 insertions(+), 263 deletions(-) diff --git a/doc/Section_commands.html b/doc/Section_commands.html index e758583e7e..80faeefde0 100644 --- a/doc/Section_commands.html +++ b/doc/Section_commands.html @@ -384,16 +384,16 @@ potentials. Click on the style itself for a full description: dpd/tstatdsmceameam/opt eam/alloyeam/alloy/opteam/fseam/fs/opt eimgaussgaybernegayberne/gpu -gran/hertz/historygran/hookegran/hooke/historylj/charmm/coul/charmm -lj/charmm/coul/charmm/implicitlj/charmm/coul/longlj/charmm/coul/long/optlj/class2 -lj/class2/coul/cutlj/class2/coul/longlj/cutlj/cut/gpu -lj/cut/optlj/cut/coul/cutlj/cut/coul/debyelj/cut/coul/long -lj/cut/coul/long/tip4plj/expandlj/gromacslj/gromacs/coul/gromacs -lj/smoothlj96/cutlubricatemeam -morsemorse/optperi/lpsperi/pmb -reaxresquaredsoftsw -tabletersofftersoff/zblyukawa -yukawa/colloid +gran/hertz/historygran/hookegran/hooke/historyhbond/dreiding/lj +hbond/dreiding/morselj/charmm/coul/charmmlj/charmm/coul/charmm/implicitlj/charmm/coul/long +lj/charmm/coul/long/optlj/class2lj/class2/coul/cutlj/class2/coul/long +lj/cutlj/cut/gpulj/cut/optlj/cut/coul/cut +lj/cut/coul/debyelj/cut/coul/longlj/cut/coul/long/tip4plj/expand +lj/gromacslj/gromacs/coul/gromacslj/smoothlj96/cut +lubricatemeammorsemorse/opt +peri/lpsperi/pmbreaxresquared +softswtabletersoff +tersoff/zblyukawayukawa/colloid

These are pair styles contributed by users, which can be used if @@ -426,8 +426,8 @@ angle potentials. Click on the style itself for a full description:

- - +
nonehybridcharmmclass2
cosinecosine/deltacosine/squaredharmonic
table +
cosinecosine/deltacosine/periodiccosine/squared
harmonictable

These are angle styles contributed by users, which can be used if @@ -460,7 +460,7 @@ description:

-
nonehybridclass2cvff
harmonic +
harmonicumbrella
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt index 9dfb33cff7..53997e819d 100644 --- a/doc/Section_commands.txt +++ b/doc/Section_commands.txt @@ -579,6 +579,8 @@ potentials. Click on the style itself for a full description: "gran/hertz/history"_pair_gran.html, "gran/hooke"_pair_gran.html, "gran/hooke/history"_pair_gran.html, +"hbond/dreiding/lj"_pair_hbond_dreiding.html, +"hbond/dreiding/morse"_pair_hbond_dreiding.html, "lj/charmm/coul/charmm"_pair_charmm.html, "lj/charmm/coul/charmm/implicit"_pair_charmm.html, "lj/charmm/coul/long"_pair_charmm.html, @@ -657,6 +659,7 @@ angle potentials. Click on the style itself for a full description: "class2"_angle_class2.html, "cosine"_angle_cosine.html, "cosine/delta"_angle_cosine_delta.html, +"cosine/periodic"_angle_cosine_periodic.html, "cosine/squared"_angle_cosine_squared.html, "harmonic"_angle_harmonic.html, "table"_angle_table.html :tb(c=4,ea=c,w=100) @@ -695,7 +698,8 @@ description: "hybrid"_improper_hybrid.html, "class2"_improper_class2.html, "cvff"_improper_cvff.html, -"harmonic"_improper_harmonic.html :tb(c=4,ea=c,w=100) +"harmonic"_improper_harmonic.html, +"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100) :line diff --git a/doc/Section_howto.html b/doc/Section_howto.html index 6fc10741c4..0924aab3ff 100644 --- a/doc/Section_howto.html +++ b/doc/Section_howto.html @@ -16,7 +16,7 @@ certain kinds of LAMMPS simulations.

4.1 Restarting a simulation
4.2 2d simulations
-4.3 CHARMM and AMBER force fields
+4.3 CHARMM, AMBER, and DREIDING force fields
4.4 Running multiple simulations from one input script
4.5 Multi-replica simulations
4.6 Granular models
@@ -31,8 +31,7 @@ certain kinds of LAMMPS simulations. 4.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
4.16 Thermostatting, barostatting and computing temperature
4.17 Walls
-4.18 Elastic constants
-4.19 Computing free energies from thermodyanmic integration
+4.18 Elastic constants

The example input scripts included in the LAMMPS distribution and highlighted in this section also show how to @@ -167,19 +166,18 @@ the same as in 3d.

-

4.3 CHARMM and AMBER force fields +

4.3 CHARMM, AMBER, and DREIDING force fields

-

There are many different ways to compute forces in the CHARMM -and AMBER molecular dynamics codes, only some of which are -available as options in LAMMPS. A force field has 2 parts: the -formulas that define it and the coefficients used for a particular -system. Here we only discuss formulas implemented in LAMMPS. Setting +

A force field has 2 parts: the formulas that define it and the +coefficients used for a particular system. Here we only discuss +formulas implemented in LAMMPS that correspond to formulas commonly +used in the CHARMM, AMBER, and DREIDING force fields. Setting coefficients is done in the input data file via the read_data command or in the input script with commands like pair_coeff or -bond_coeff. See this section for -additional tools that can use CHARMM or AMBER to assign force field -coefficients and convert their output into LAMMPS input. +bond_coeff. See this section +for additional tools that can use CHARMM or AMBER to assign force +field coefficients and convert their output into LAMMPS input.

See (MacKerell) for a description of the CHARMM force field. See (Cornell) for a description of the AMBER force @@ -193,16 +191,56 @@ field. with common options in CHARMM or AMBER. See each command's documentation for the formula it computes.

-