Added source code and documentation for USER-CGDNA

\documentclass[12pt]{article}

\begin{document}

$$ 

  E = - \frac{\epsilon}{2} \ln \left[ 1 - \left(\frac{r-r0}{\Delta}\right)^2\right]

$$

\end{document}

"PERI"_#PERI, Peridynamics models, Mike Parks (Sandia), "pair_style peri"_pair_peri.html, peri, -

"POEMS"_#POEMS, coupled rigid body motion, Rudra Mukherjee (JPL), "fix poems"_fix_poems.html, rigid, lib/poems

"PYTHON"_#PYTHON, embed Python code in an input script, -, "python"_python.html, python, lib/python

"REAX"_#REAX, ReaxFF potential, Aidan Thompson (Sandia), "pair_style reax"_pair_reax.html, reax,  lib/reax

"REPLICA"_#REPLICA, multi-replica methods, -, "Section 6.6.5"_Section_howto.html#howto_5, tad, -

"RIGID"_#RIGID, rigid bodies, -, "fix rigid"_fix_rigid.html, rigid, -

"SHOCK"_#SHOCK, shock loading methods, -, "fix msst"_fix_msst.html, -, -

"USER-ATC"_#USER-ATC, atom-to-continuum coupling, Jones & Templeton & Zimmerman (1), "fix atc"_fix_atc.html, USER/atc, "atc"_atc, lib/atc

"USER-AWPMD"_#USER-AWPMD, wave-packet MD, Ilya Valuev (JIHT), "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, -, lib/awpmd

"USER-CG-CMM"_#USER-CG-CMM, coarse-graining model, Axel Kohlmeyer (Temple U), "pair_style lj/sdk"_pair_sdk.html, USER/cg-cmm, "cg"_cg, -

"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, Oliver Henrich (U Edinburgh), src/USER-CGDNA/README, USER/cgdna, -, -

"USER-COLVARS"_#USER-COLVARS, collective variables, Fiorin & Henin & Kohlmeyer (2), "fix colvars"_fix_colvars.html, USER/colvars, "colvars"_colvars, lib/colvars

"USER-DIFFRACTION"_#USER-DIFFRACTION, virutal x-ray and electron diffraction, Shawn Coleman (ARL),"compute xrd"_compute_xrd.html, USER/diffraction, -, -

"USER-DPD"_#USER-DPD, reactive dissipative particle dynamics (DPD), Larentzos & Mattox & Brennan (5), src/USER-DPD/README, USER/dpd, -, -

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USER-CGDNA package :link(USER-CGDNA),h5

Contents: The CGDNA package implements coarse-grained force fields

for single- and double-stranded DNA. This is at the moment mainly

the oxDNA model, developed by Doye, Louis and Ouldridge at the 

University of Oxford. 

The package also contains Langevin-type rigid-body integrators

with improved stability.

See these doc pages to get started:

"bond_style oxdna_fene"_bond_oxdna_fene.html

"pair_style oxdna_excv"_pair_oxdna_excv.html

"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

Supporting info: /src/USER-CGDNA/README, "bond_style oxdna_fene"_bond_oxdna_fene.html,

"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

Author: Oliver Henrich at the University of Edinburgh, UK (o.henrich

at epcc.ed.ac.uk or ohenrich at ph.ed.ac.uk). Contact him directly 

if you have any questions. 

:line

USER-COLVARS package :link(USER-COLVARS),h5

Contents: COLVARS stands for collective variables which can be used to

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

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bond_style oxdna_fene command :h3

[Syntax:]

bond_style oxdna_fene :pre

[Examples:]

bond_style oxdna_fene

bond_coeff * 2.0 0.25 0.7525 :pre

[Description:]

The {oxdna_fene} bond style uses the potential

:c,image(Eqs/bond_oxdna_fene.jpg)

to define a modified finite extensible nonlinear elastic (FENE) potential

"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone

in the oxDNA force field for coarse-grained modelling of DNA. 

The following coefficients must be defined for the bond type via the

"bond_coeff"_bond_coeff.html command as given in the above example, or in

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

or "read_restart"_read_restart.html commands:

epsilon (energy)

Delta (distance)

r0 (distance) :ul

NOTE: This bond style has to be used together with the corresponding oxDNA pair styles

for excluded volume interaction {oxdna_excv}, stacking {oxdna_stk}, cross-stacking {oxdna_xstk}

and coaxial stacking interaction {oxdna_coaxstk} as well as hydrogen-bonding interaction {oxdna_hbond} (see also documentation of 

"pair_style oxdna_excv"_pair_oxdna_excv.html). The coefficients 

in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.

Example input and data files can be found in /examples/USER/cgdna/examples/duplex1/ and /duplex2/.

A simple python setup tool which creates single straight or helical DNA strands,

DNA duplexes or arrays of DNA duplexes can be found in /examples/USER/cgdna/util/.

A technical report with more information on the model, the structure of the input file,

the setup tool and the performance of the LAMMPS-implementation of oxDNA

can be found "here"_PDF/USER-CGDNA-overview.pdf.

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[Restrictions:]

This bond style can only be used if LAMMPS was built with the

USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making

LAMMPS"_Section_start.html#start_3 section for more info on packages.

[Related commands:]

"pair_style oxdna_excv"_pair_oxdna_excv.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html 

[Default:] none

:line

:link(oxdna_fene)

[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)

:link(ld,Manual.html)

:link(lc,Section_commands.html#comm)

:line

fix nve/dot command :h3

[Syntax:]

fix ID group-ID nve/dot :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l

nve/dot = style name of this fix command :l

:ule

[Examples:]

fix 1 all nve/dot :pre

[Description:]

Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack

to a group of atoms, but without Langevin dynamics. 

This command performs Molecular dynamics (MD)

via a velocity-Verlet algorithm and an evolution operator that rotates 

the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller. 

This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html

without damping and noise and can be used to determine the stability range 

in a NVE ensemble prior to using the Langevin-type DOTC-integrator

(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).

The command is equivalent to the "fix nve"_fix_nve.html.

The particles are always considered to have a finite size.

An example input file can be found in /examples/USER/cgdna/examples/duplex1/.

A technical report with more information on this integrator can be found

"here"_PDF/USER-CGDNA-overview.pdf.

:line

[Restrictions:]

These pair styles can only be used if LAMMPS was built with the

USER-CGDNA package and the MOLECULE and ASPHERE package.  See the "Making

LAMMPS"_Section_start.html#start_3 section for more info on packages.

[Related commands:]

"fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "fix nve"_fix_nve.html

[Default:] none

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:link(Davidchack)

[(Davidchack)] R.L Davidchack, T.E. Ouldridge, and M.V. Tretyakov. J. Chem. Phys. 142, 144114 (2015).

:link(Miller)

[(Miller)] T. F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).