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patch_28Ma
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patch_31Ma
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@ -1,7 +1,7 @@
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<!-- HTML_ONLY -->
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<HEAD>
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<TITLE>LAMMPS Users Manual</TITLE>
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<META NAME="docnumber" CONTENT="28 Mar 2017 version">
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<META NAME="docnumber" CONTENT="31 Mar 2017 version">
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<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
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<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
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</HEAD>
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@ -21,7 +21,7 @@
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<H1></H1>
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LAMMPS Documentation :c,h3
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28 Mar 2017 version :c,h4
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31 Mar 2017 version :c,h4
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Version info: :h4
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@ -1686,7 +1686,7 @@ nph) and Berendsen:
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The "fix npt"_fix_nh.html commands include a Nose-Hoover thermostat
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and barostat. "Fix nph"_fix_nh.html is just a Nose/Hoover barostat;
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it does no thermostatting. Both "fix nph"_fix_nh.html and "fix
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press/bernendsen"_fix_press_berendsen.html can be used in conjunction
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press/berendsen"_fix_press_berendsen.html can be used in conjunction
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with any of the thermostatting fixes.
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As with the thermostats, "fix npt"_fix_nh.html and "fix
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@ -90,8 +90,8 @@ the difference between the {charmm} and {charmmfsh} styles is in the
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computation of the 1-4 non-bond interactions, though only if the
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distance between the two atoms is within the switching region of the
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pairwise potential defined by the corresponding CHARMM pair style,
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i.e. between the inner and outer cutoffs specified for the pair style.
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The {charmmfsh} style should only be used when using the "pair_style
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i.e. within the outer cutoff specified for the pair style. The
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{charmmfsh} style should only be used when using the "pair_style
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lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
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pairwise calculations consistent. Use the {charmm} style with
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long-range Coulombics or the older "pair_style
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@ -464,6 +464,7 @@ pair_nb3b_harmonic.html
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pair_nm.html
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pair_none.html
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pair_oxdna.html
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pair_oxdna2.html
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pair_peri.html
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pair_polymorphic.html
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pair_quip.html
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@ -49,8 +49,8 @@ args = list of arguments for a particular style :ul
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0
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pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0 7.0 9.0
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pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0
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pair_style lj/charmmfsw/coul/charmmfsh 10.0 12.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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@ -29,19 +29,29 @@ action () {
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# list of files with dependcies
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action bond_oxdna_fene.cpp bond_fene.h
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action bond_oxdna2_fene.cpp bond_fene.h
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action bond_oxdna_fene.h bond_fene.h
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action bond_oxdna2_fene.h bond_fene.h
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action fix_nve_dotc_langevin.cpp atom_vec_ellipsoid.h
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action fix_nve_dotc_langevin.h atom_vec_ellipsoid.h
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action fix_nve_dot.cpp atom_vec_ellipsoid.h
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action fix_nve_dot.h atom_vec_ellipsoid.h
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action mf_oxdna.h atom_vec_ellipsoid.h
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action pair_oxdna_coaxstk.cpp atom_vec_ellipsoid.h
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action pair_oxdna2_coaxstk.cpp atom_vec_ellipsoid.h
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action pair_oxdna_coaxstk.h atom_vec_ellipsoid.h
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action pair_oxdna2_coaxstk.h atom_vec_ellipsoid.h
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action pair_oxdna_excv.cpp atom_vec_ellipsoid.h
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action pair_oxdna2_excv.cpp atom_vec_ellipsoid.h
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action pair_oxdna_excv.h atom_vec_ellipsoid.h
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action pair_oxdna2_excv.h atom_vec_ellipsoid.h
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action pair_oxdna_hbond.cpp atom_vec_ellipsoid.h
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action pair_oxdna_hbond.h atom_vec_ellipsoid.h
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action pair_oxdna_stk.cpp atom_vec_ellipsoid.h
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action pair_oxdna2_stk.cpp atom_vec_ellipsoid.h
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action pair_oxdna_stk.h atom_vec_ellipsoid.h
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action pair_oxdna2_stk.h atom_vec_ellipsoid.h
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action pair_oxdna_xstk.cpp atom_vec_ellipsoid.h
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action pair_oxdna_xstk.h atom_vec_ellipsoid.h
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action pair_oxdna2_dh.cpp atom_vec_ellipsoid.h
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action pair_oxdna2_dh.h atom_vec_ellipsoid.h
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@ -2,9 +2,9 @@ This package contains a LAMMPS implementation of coarse-grained
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models of DNA, which can be used to model sequence-specific
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DNA strands.
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See the doc pages and [1,2] for the individual bond and pair styles.
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See the doc pages and [1,2,3] for the individual bond and pair styles.
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The packages contains also a new Langevin-type rigid-body integrator,
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which has also its own doc page and is explained in [3].
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which has also its own doc page and is explained in [4].
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[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
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and thermodynamic properties of a coarse-grained DNA model",
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@ -13,16 +13,20 @@ J. Chem. Phys. 134, 085101 (2011).
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[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
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self-assembly, DPhil. University of Oxford (2011).
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[3] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
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[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
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Improved Structural Properties and Salt Dependence into a Coarse-Grained
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Model of DNA, J. Chem. Phys. 142, 234901 (2015).
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[4] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
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gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
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144114 (2015).
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Example input and data files can be found in
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/examples/USER/cgdna/examples/duplex1/ and /duplex2/. A simple python
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setup tool which creates single straight or helical DNA strands as
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well as DNA duplexes and arrays of duplexes can be found in
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/examples/USER/cgdna/util/. A technical report with more information
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on the model, the structure of the input and data file, the setup tool
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/examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/. Python setup
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tools which create single straight or helical DNA strands as
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well as DNA duplexes or arrays of duplexes can be found in
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/examples/USER/cgdna/util/. A technical report with more information
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on the models, the structure of the input and data file, the setup tool
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and the performance of the LAMMPS-implementation of oxDNA can be found
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in /doc/src/PDF/USER-CGDNA-overview.pdf.
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@ -35,6 +39,7 @@ of the LAMMPS manual).
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The creator of this package is:
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Dr Oliver Henrich
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University of Strathclyde, UK
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University of Edinburgh, UK
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ohenrich@ph.ed.ac.uk
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o.henrich@epcc.ed.ac.uk
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@ -45,6 +50,8 @@ o.henrich@epcc.ed.ac.uk
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bond_oxdna_fene.cpp: backbone connectivity, a modified FENE potential
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bond_oxdna2_fene.cpp: corresponding bond style in oxDNA2 (see [3])
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** Pair styles provided by this package:
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pair_oxdna_excv.cpp: excluded volume interaction between the nucleotides
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@ -59,6 +66,13 @@ pair_oxdna_xstk.cpp: cross-stacking interaction between nucleotides
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pair_oxdna_coaxstk.cpp: coaxial stacking interaction between nucleotides
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pair_oxdna2_excv.cpp, pair_oxdna2_stk.cpp, pair_oxdna2_coaxstk.cpp:
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corresponding pair styles in oxDNA2 (see [3])
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pair_oxdna2_dh.cpp: Debye-Hueckel electrostatic interaction between backbone
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sites
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** Fixes provided by this package:
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fix_nve_dotc_langevin.cpp: fix for Langevin-type rigid body integrator "C"
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@ -254,10 +254,9 @@ double FixHalt::tlimit()
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bigint final = update->firststep +
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static_cast<bigint> (tratio*value/cpu * elapsed);
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nextstep = (final/nevery)*nevery + nevery;
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if (nextstep == update->ntimestep) nextstep += nevery;
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tratio = 1.0;
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}
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//printf("EVAL %ld %g %d\n",update->ntimestep,cpu,nevery);
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return cpu;
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}
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@ -1 +1 @@
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#define LAMMPS_VERSION "28 Mar 2017"
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#define LAMMPS_VERSION "31 Mar 2017"
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Block a user