Merge pull request #440 from ohenrich/user-cgdna (4466d9fb) · Commits · 郑智淋 / lammps

doc/src/lammps.book

+1 −0

Original line number	Diff line number	Diff line
		@@ -464,6 +464,7 @@ pair_nb3b_harmonic.html
		pair_nm.html
		pair_none.html
		pair_oxdna.html
		pair_oxdna2.html
		pair_peri.html
		pair_polymorphic.html
		pair_quip.html

src/USER-CGDNA/Install.sh

+10 −0

Original line number	Diff line number	Diff line
		@@ -29,19 +29,29 @@ action () {
		# list of files with dependcies

		action bond_oxdna_fene.cpp bond_fene.h
		action bond_oxdna2_fene.cpp bond_fene.h
		action bond_oxdna_fene.h bond_fene.h
		action bond_oxdna2_fene.h bond_fene.h
		action fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
		action fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
		action fix_nve_dot.cpp atom_vec_ellipsoid.h
		action fix_nve_dot.h atom_vec_ellipsoid.h
		action mf_oxdna.h atom_vec_ellipsoid.h
		action pair_oxdna_coaxstk.cpp atom_vec_ellipsoid.h
		action pair_oxdna2_coaxstk.cpp atom_vec_ellipsoid.h
		action pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
		action pair_oxdna2_coaxstk.h atom_vec_ellipsoid.h
		action pair_oxdna_excv.cpp atom_vec_ellipsoid.h
		action pair_oxdna2_excv.cpp atom_vec_ellipsoid.h
		action pair_oxdna_excv.h atom_vec_ellipsoid.h
		action pair_oxdna2_excv.h atom_vec_ellipsoid.h
		action pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
		action pair_oxdna_hbond.h atom_vec_ellipsoid.h
		action pair_oxdna_stk.cpp atom_vec_ellipsoid.h
		action pair_oxdna2_stk.cpp atom_vec_ellipsoid.h
		action pair_oxdna_stk.h atom_vec_ellipsoid.h
		action pair_oxdna2_stk.h atom_vec_ellipsoid.h
		action pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
		action pair_oxdna_xstk.h atom_vec_ellipsoid.h
		action pair_oxdna2_dh.cpp atom_vec_ellipsoid.h
		action pair_oxdna2_dh.h atom_vec_ellipsoid.h

src/USER-CGDNA/README

+22 −8

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		@@ -2,9 +2,9 @@ This package contains a LAMMPS implementation of coarse-grained
		models of DNA, which can be used to model sequence-specific
		DNA strands.

		See the doc pages and [1,2] for the individual bond and pair styles.
		See the doc pages and [1,2,3] for the individual bond and pair styles.
		The packages contains also a new Langevin-type rigid-body integrator,
		which has also its own doc page and is explained in [3].
		which has also its own doc page and is explained in [4].

		[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
		and thermodynamic properties of a coarse-grained DNA model",
		@@ -13,16 +13,20 @@ J. Chem. Phys. 134, 085101 (2011).
		[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
		self-assembly, DPhil. University of Oxford (2011).

		[3] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
		[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
		Improved Structural Properties and Salt Dependence into a Coarse-Grained
		Model of DNA, J. Chem. Phys. 142, 234901 (2015).

		[4] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
		gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
		144114 (2015).

		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 as
		well as DNA duplexes and arrays of duplexes can be found in
		/examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. Python setup
		tools which create single straight or helical DNA strands as
		well as DNA duplexes or arrays of duplexes can be found in
		/examples/USER/cgdna/util/. A technical report with more information
		on the model, the structure of the input and data file, the setup tool
		on the models, the structure of the input and data file, the setup tool
		and the performance of the LAMMPS-implementation of oxDNA can be found
		in /doc/src/PDF/USER-CGDNA-overview.pdf.

		@@ -35,6 +39,7 @@ of the LAMMPS manual).
		The creator of this package is:

		Dr Oliver Henrich
		University of Strathclyde, UK
		University of Edinburgh, UK
		ohenrich@ph.ed.ac.uk
		o.henrich@epcc.ed.ac.uk
		@@ -45,6 +50,8 @@ o.henrich@epcc.ed.ac.uk

		bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential

		bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3])

		** Pair styles provided by this package:

		pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides
		@@ -59,6 +66,13 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides

		pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides


		pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp:
		corresponding pair styles in oxDNA2 (see [3])

		pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone
		sites

		** Fixes provided by this package:

		fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C"

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