jianmu
/
lammps
forked from lijiext/lammps
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added reference to implementation paper

This commit is contained in:
Oliver Henrich 2018-05-07 18:13:18 +01:00
parent eeee2d3026
commit 722549965e
5 changed files with 41 additions and 20 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

BIN
doc/src/PDF/USER-CGDNA.pdf Normal file
View File

Binary file not shown.

11
doc/src/bond_oxdna.txt
View File

@ -51,9 +51,11 @@ The coefficients in the above example have to be kept fixed and cannot be change
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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.
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -72,6 +74,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(oxdna_fene)
[(Ouldridge)] T.E. Ouldridge, A.A. Louis, J.P.K. Doye, J. Chem. Phys. 134, 085101 (2011).

11
doc/src/pair_oxdna.txt
View File

@ -71,9 +71,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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.
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -92,6 +94,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(Sulc1)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

11
doc/src/pair_oxdna2.txt
View File

@ -77,9 +77,11 @@ the temperature coefficients have to be matched to the one used in the fix.
Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
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.
Please cite "(Henrich)"_#Henrich and the relevant oxDNA articles in any publication that uses this implementation.
The article contains more information on the model, the structure of the input file, the setup tool
and the performance of the LAMMPS-implementation of oxDNA.
The preprint version of the article can be found "here"_PDF/USER-CGDNA.pdf.
:line
@ -98,6 +100,9 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
:line
:link(Henrich)
[(Henrich)] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
:link(Sulc2)
[(Sulc)] P. Sulc, F. Romano, T.E. Ouldridge, L. Rovigatti, J.P.K. Doye, A.A. Louis, J. Chem. Phys. 137, 135101 (2012).

28
src/USER-CGDNA/README
View File

@ -2,22 +2,29 @@ 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 [1,2,3] 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 [4].
Please cite [1] and the relevant oxDNA articles in any publication
that uses this package.
[1] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
See the doc pages and [2,3,4] 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 [5].
[1] O. Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge,
"Coarse-grained simulation of DNA using LAMMPS",
Eur. Phys. J. E 41, 57 (2018).
[2] T. Ouldridge, A. Louis, J. Doye, "Structural, mechanical,
and thermodynamic properties of a coarse-grained DNA model",
J. Chem. Phys. 134, 085101 (2011).
[2] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
[3] T.E. Ouldridge, Coarse-grained modelling of DNA and DNA
self-assembly, DPhil. University of Oxford (2011).
[3] B.E. Snodin, F. Randisi, M. Mosayebi, et al., Introducing
[4] 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
[5] R. Davidchack, T. Ouldridge, M. Tretyakov, "New Langevin and
gradient thermostats for rigid body dynamics", J. Chem. Phys. 142,
144114 (2015).
@ -28,7 +35,7 @@ well as DNA duplexes or arrays of duplexes can be found in
/examples/USER/cgdna/util/. A technical report with more information
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.
in /doc/src/PDF/USER-CGDNA.pdf.
IMPORTANT NOTE: This package can only be used if LAMMPS is compiled
with the MOLECULE and ASPHERE packages. These should be included in
@ -40,9 +47,8 @@ The creator of this package is:
Dr Oliver Henrich
University of Strathclyde, Glasgow, UK
oliver.henrich at strath.ac.uk
University of Edinburgh, UK
ohenrich at staffmail.ed.ac.uk
oliver d o t henrich a t strath d o t ac d o t uk
--------------------------------------------------------------------------