new CHARMM pair styles with force swithing/shifting

"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,

"lj/charmm/coul/long (giko)"_pair_charmm.html,

"lj/charmm/coul/msm"_pair_charmm.html,

"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,

"lj/charmmfsw/coul/long"_pair_charmm.html,

"lj/class2 (gko)"_pair_class2.html,

"lj/class2/coul/cut (ko)"_pair_class2.html,

"lj/class2/coul/long (gko)"_pair_class2.html,

"zero"_dihedral_zero.html,

"hybrid"_dihedral_hybrid.html,

"charmm (ko)"_dihedral_charmm.html,

"charmmfsh"_dihedral_charmm.html,

"class2 (ko)"_dihedral_class2.html,

"harmonic (io)"_dihedral_harmonic.html,

"helix (o)"_dihedral_helix.html,

accelerate: run with various acceleration options (OpenMP, GPU, Phi)

balance:  dynamic load balancing, 2d system

body:     body particles, 2d system

cmap:     CMAP 5-body contributions to CHARMM force field

colloid:  big colloid particles in a small particle solvent, 2d system

comb:     models using the COMB potential

coreshell: core/shell model using CORESHELL package

controller: use of fix controller as a thermostat

crack:    crack propagation in a 2d solid

deposit:  deposit atoms and molecules on a surface

dipole:   point dipolar particles, 2d system

ellipse:  ellipsoidal particles in spherical solvent, 2d system

flow:     Couette and Poiseuille flow in a 2d channel

friction: frictional contact of spherical asperities between 2d surfaces

gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command

granregion: use of fix wall/region/gran as boundary on granular particles

hugoniostat: Hugoniostat shock dynamics

indent:   spherical indenter into a 2d solid

kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)

melt:     rapid melt of 3d LJ system

micelle:  self-assembly of small lipid-like molecules into 2d bilayers

min:      energy minimization of 2d LJ melt

mscg:     parameterize a multi-scale coarse-graining (MSCG) model

msst:     MSST shock dynamics

nb3b:     use of nonbonded 3-body harmonic pair style

neb:      nudged elastic band (NEB) calculation for barrier finding

srd:      stochastic rotation dynamics (SRD) particles as solvent

streitz:  use of Streitz/Mintmire potential with charge equilibration

tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si

vashishta: use of the Vashishta potential :tb(s=:)

vashishta: use of the Vashishta potential

voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)

Here is how you can run and visualize one of the sample problems:

"bond_style"_bond_harmonic.html harmonic

"angle_style"_angle_charmm.html charmm

"dihedral_style"_dihedral_charmm.html charmmfsh

"dihedral_style"_dihedral_charmm.html charmm

"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh

"pair_style"_pair_charmm.html lj/charmmfsw/coul/long

"pair_style"_pair_charmm.html lj/charmm/coul/charmm

"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit

"pair_style"_pair_charmm.html lj/charmm/coul/long :ul

"special_bonds"_special_bonds.html charmm

"special_bonds"_special_bonds.html amber :ul

NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were

released in March 2017.  We recommend they be used instead of the

older {charmm} styles.  See discussion of the differences on the "pair

charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html

doc pages.

DREIDING is a generic force field developed by the "Goddard

group"_http://www.wag.caltech.edu at Caltech and is useful for

predicting structures and dynamics of organic, biological and

    N = # of extra degrees of freedom to subtract

  {extra} syntax is identical to {extra/dof}, will be disabled at some point

  {dynamic/dof} value = {yes} or {no}

    yes/no = do or do not recompute the number of atoms contributing to the temperature

    yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature

  {dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre

:ule

temp/asphere"_compute_temp_asphere.html command for an example.

The {dynamic/dof} or {dynamic} keyword determines whether the number

of atoms N in the compute group is re-computed each time a temperature

is computed.  Only compute styles that calculate a temperature use

this option.  By default, N is assumed to be constant.  If you are

adding atoms to the system (see the "fix pour"_fix_pour.html, "fix

deposit"_fix_deposit.html and "fix gcmc"_fix_gcmc.html commands) or

expect atoms to be lost (e.g. due to evaporation), then this option

should be used to insure the temperature is correctly normalized.

of atoms N in the compute group and their associated degrees of

freedom are re-computed each time a temperature is computed.  Only

compute styles that calculate a temperature use this option.  By

default, N and their DOF are assumed to be constant.  If you are

adding atoms or molecules to the system (see the "fix

pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix

gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost

(e.g. due to exiting the simulation box or via "fix

evaporation"_fix_evaporation.html), then this option should be used to

insure the temperature is correctly normalized.

NOTE: The {extra} and {dynamic} keywords should not be used as they

are deprecated (March 2017) and will eventually be disabled.  Instead,

dihedral_style charmm/intel command :h3

dihedral_style charmm/kk command :h3

dihedral_style charmm/omp command :h3

dihedral_style charmmfsh command :h3

[Syntax:]

dihedral_style charmm :pre

dihedral_style style :pre

style = {charmm} or {charmmfsh} :ul

[Examples:]

dihedral_style charmm

dihedral_style charmmfsh

dihedral_coeff  1 0.2 1 180 1.0

dihedral_coeff  2 1.8 1   0 1.0

dihedral_coeff  1 3.1 2 180 0.5 :pre

[Description:]

The {charmm} dihedral style uses the potential

The {charmm} and {charmmfsh} dihedral styles use the potential

:c,image(Eqs/dihedral_charmm.jpg)

"(Cornell)"_#dihedral-Cornell for a description of the AMBER force

field.

NOTE: The newer {charmmfsh} style was released in March 2017.  We

recommend it be used instead of the older {charmm} style when running

a simulation with the CHARMM force field.  See the discussion below

and more details on the "pair_style charmm"_pair_charmm.html doc page.

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

the data file or restart files read by the "read_data"_read_data.html

default). Otherwise 1-4 non-bonded interactions in dihedrals will be

computed twice.

Also note that for AMBER force fields, which use pair styles with

"lj/cut", the special_bonds 1-4 scaling factor should be set to the

AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors

(4th coeff above) must be set to 0.0. In this case, you can use any

pair style you wish, since the dihedral does not need any

Lennard-Jones parameter information and will not compute any 1-4

non-bonded interactions.

For simulations using the CHARMM force field, the difference between

the {charmm} and {charmmfsh} styles is in the computation of the 1-4

non-bond interactions, if the distance between the two atoms is within

the switching distance of the pairwise potential defined by the

corresponding CHARMM pair style, i.e. between the inner and outer

cutoffs specified for the pair style.  See the discussion on the

"CHARMM pair_style"_pair_charmm.html doc page for details.

Note that for AMBER force fields, which use pair styles with "lj/cut",

the special_bonds 1-4 scaling factor should be set to the AMBER

defaults (1/2 and 5/6) and all the dihedral weighting factors (4th

coeff above) must be set to 0.0. In this case, you can use any pair

style you wish, since the dihedral does not need any Lennard-Jones

parameter information and will not compute any 1-4 non-bonded

interactions.  Likewise the {charmm} or {charmmfsh} styles are

identical in this case since no 1-4 non-bonded interactions are

computed.

:line