add moltemplate version 2017-8-22

tools/moltemplate/LICENSE.md

+Modified BSD License (BSD-3-Clause)
+====================
+
+_Copyright © `2012`, `University of California, Santa Barbara`_  
+_All rights reserved._
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright
+   notice, this list of conditions and the following disclaimer in the
+   documentation and/or other materials provided with the distribution.
+3. Neither the name of the copyright holders nor the names of its
+   contributors may be used to endorse or promote products derived from 
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS “AS IS”
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE.

tools/moltemplate/README.md

+Moltemplate
+===========
+
+##  Description
+
+Moltemplate is a cross-platform text-based molecule builder for LAMMPS.
+
+## Typical usage
+
+    moltemplate.sh [-atomstyle style] [-pdb/-xyz coord_file] [-vmd] system.lt
+
+## Web page
+
+Documentation, examples, and supporting code can be downloaded at:
+
+http://www.moltemplate.org
+
+## Requirements
+
+Moltemplate requires the Bourne-shell, and a recent version of python
+(2.7, 3.0 or higher), and can run on OS X, linux, or windows. (...if a
+suitable shell environment has been installed.  See below.)
+
+
+## INSTALLATION INSTRUCTIONS
+
+This directory should contain 3 folders:
+
+    moltemplate/                  <-- source code and force fields
+    doc/                          <-- the moltemplate reference manual
+    examples/                     <-- examples built with moltemplate
+
+There are two ways to install moltemplate:
+
+## Installation using pip
+If you are familiar with pip, then run the following command from within the directory where this README file is located:
+
+    pip install .
+
+If you receive an error regarding permissions, then run pip with the "--user" argument:
+
+    pip install . --user
+
+Make sure that your default pip install bin directory is in your PATH.  (This is usually something like ~/.local/bin/ or ~/anaconda3/bin/.  If you have installed anaconda, this will be done for you automatically.)  Later, you can uninstall moltemplate using:
+
+    pip uninstall moltemplate
+
+If you continue to run into difficulty, try installing moltemplate into a temporary virtual environment by installing "virtualenv", downloading moltemplate (to "~/moltemplate" in the example below), and running these commands:
+
+    cd ~/moltemplate
+    virtualenv venv
+    source venv/bin/activate
+    pip install .
+    #(now do something useful with moltemplate...)
+
+(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate.)  If all this fails, then try installing moltemplate by manually updating your \$PATH environment variable.  Instructions for doing that are included below.
+
+## Manual installation:
+
+Alternatively, you can edit your $PATH environment variable manually to 
+include the subdirectory where the "moltemplate.sh" script is located,
+as well as the subdirectory where most of the python scripts are located.
+Suppose the directory with this README file is named "moltemplate"
+and is located in your home directory:
+
+If you use the bash shell, typically you would edit your
+`~/.profile`, `~/.bash_profile` or `~/.bashrc` files
+to contain the following lines:
+
+    export PATH="$PATH:$HOME/moltemplate/moltemplate"
+    export PATH="$PATH:$HOME/moltemplate/moltemplate/scripts"
+
+If you use the tcsh shell, typically you would edit your
+`~/.login`, `~/.cshrc`, or `~/.tcshrc` files to contain the following lines:
+
+    setenv PATH "$PATH:$HOME/moltemplate/moltemplate"
+    setenv PATH "$PATH:$HOME/moltemplate/moltemplate/scripts"
+
+After making these changes, you may need to start a new terminal (shell) for the changes to take effect.  If you do not know what a `PATH` environment variable is and are curious, read:
+    http://www.linfo.org/path_env_var.html
+(I receive this question often.)
+
+
+### WINDOWS installation suggestions
+
+You can install both moltemplate and LAMMPS in windows, but you will first need to install the BASH shell environment on your computer.  If you are using Windows 10 or later, try installing the "Windows Subsystem for Linux (WSL)"
+
+https://solarianprogrammer.com/2017/04/15/install-wsl-windows-subsystem-for-linux/
+https://msdn.microsoft.com/en-us/commandline/wsl/faq
+
+If you are using an older version of windows, try following the tutorial written by Yanqing Fu instead:
+
+https://sourceforge.net/p/lammps/mailman/message/32599824/
+
+To use LAMMPS and moltemplate, You will also need to install (and learn how to use) a text editor.  (Word, Wordpad, and Notepad will not work.)  Popular free text editors which you can safely install and run from within the WSL terminal include: **nano**, **ne**, **emacs**, **vim**, and **jove**.  (Unfortunately, as of 2017-5-17, [graphical unix-friendly text editors such as Atom, VSCode, Notepad++, and sublime won't work with WSL, and may cause file system corruption.  Avoid these editors for now.](https://www.reddit.com/r/bashonubuntuonwindows/comments/6bu1d1/since_we_shouldnt_edit_files_stored_in_wsl_with/))
+
+## License
+
+Moltemplate is available under the terms of the open-source 3-clause BSD
+license.  (See `LICENSE.md`.)

tools/moltemplate/doc/moltemplate_manual_src/README.txt

+To create the file "moltemplate_manual.pdf", install pdflatex and run
+these commands:
+
+pdflatex moltemplate_manual
+pdflatex moltemplate_manual
+bibtex moltemplate_manual
+bibtex moltemplate_manual
+pdflatex moltemplate_manual
+pdflatex moltemplate_manual
+

tools/moltemplate/doc/moltemplate_manual_src/refs.bib

+@STRING{CELL="Cell"}
+@STRING{JMB="J. Mol. Biol."}
+@STRING{BIOCHEMISTRY="Biochemistry"}
+@STRING{BIOPHYSICALCHEMISTRY="Biophys. Chem."}
+@STRING{JCP="J. Chem. Phys."}
+@STRING{PNAS="Proc. Natl. Acad. Sci. USA"}
+@STRING{BIOPOLYMERS="Biopolymers"}
+@STRING{SCIENCE="Science"}
+@STRING{MMBR="Microbiol. Mol. Biol. R."}
+@STRING{NATURE="Nature"}
+@STRING{NATSTRUCTBIOL="Nat. Struct. Biol."}
+@STRING{NATBIOTECHNOL="Nat. Biotechnol."}
+@STRING{JBIOLCHEM="J. Biol. Chem."}
+@STRING{JSTRUCTBIOL="J. Struct. Biol."}
+@STRING{FOLDINGANDDESIGN="Folding and Design"}
+%@STRING{PROTSTRFUNCGEN="Prot. Str. Func. Gen."}
+@STRING{PROTSTRFUNCGEN="Proteins"}
+@STRING{PRL="Phys. Rev. Lett."}
+@STRING{TIBS="Trends in Biochem. Sci."}
+@STRING{EMBOJ="EMBO J."}
+@STRING{FEBS="FEBS Letters"}
+@STRING{FASEB="FASEB"}
+@STRING{JBIOCHEMTOXICOL="J. Biochem. Toxicol."}
+@STRING{CRBMB="Crit. Rev. Biochem. Mol. Biol."}
+@STRING{CHEMREV="Chem. Rev."}
+@STRING{ANNUREVBIOCHEM="Annu. Rev. Biochem."}
+% ------------------  books ----------------------
+
+
+@INBOOK{vanKampenBook,
+   AUTHOR="van Kampen, N. G.",
+   TITLE="Stochastic Processes in Physics and Chemistry, 2nd Edition",
+   PUBLISHER="North Holland",
+   PAGES={96--127},
+   MONTH="July",
+   DAY="1",
+   YEAR=2001
+}
+
+
+@ARTICLE{LAMMPS,
+   AUTHOR="S. Plimpton", 
+   TITLE="Fast Parallel Algorithms for Short-Range Molecular Dynamics", 
+   JOURNAL="J. Comp. Phys.", 
+   VOLUME=117,
+   PAGES={1--19},
+   YEAR="1995",
+   NOTE={\url{http://lammps.sandia.gov/}}
+}
+
+
+@ARTICLE{packmol,
+  AUTHOR="Martínez, L. and Andrade, R. and Brigin, E. G. and Martínez, J. M.",
+  TITLE="Packmol: A package for building initial configurations for molecular dynamics simulations.",
+  JOURNAL="J. Comp. Chem.",
+  VOLUME=30,
+  NUMBER=13,
+  PAGES={2157--2164},
+  YEAR=2009,
+  NOTE={\url{http://www.ime.unicamp.br/~martinez/packmol/}}
+}
+
+
+%% The primary VMD citation, should be used by all publications using VMD
+@article{VMD,
+  author={William Humphrey and Andrew Dalke and Klaus Schulten},
+  title={{VMD} -- {V}isual {M}olecular {D}ynamics},
+  journal={Journal of Molecular Graphics},
+  year=1996,
+  volume=14,
+  pages={33-38},
+  tbstatus={Published.},
+  techrep={},
+  tbreference={222},
+  NOTE={\url{http://www.ks.uiuc.edu/Research/vmd}}
+}
+
+%% Interactive Molecular Dynamics, cited by papers doing IMD simulations
+@inproceedings{VMDIMD,
+  author={John Stone and Justin Gullingsrud and Paul Grayson and Klaus Schulten},
+  title={A System for Interactive Molecular Dynamics Simulation},
+  booktitle={2001 ACM Symposium on Interactive 3D Graphics},
+  publisher={ACM SIGGRAPH},
+  address={New York},
+  editor={John F. Hughes and Carlo H. S\'equin},
+  pages={191-194},
+  year={2001},
+  note={},
+  tbreference={304},
+  tbstatus={Published.},
+  annote={This symposium took place between March 19-21, 2001. {ISBN} 1-58113-292-1.}
+}
+
+@MISC{topotools,
+  AUTHOR="Axel Kohlmeyer",
+  TITLE="{The TopoTools VMD plugin}",
+  HOWPUBLISHED={\url{http://sites.google.com/site/akohlmey/software/topotools/}}
+}
+
+
+@MISC{pizzapy,
+  AUTHOR="Steve Plimpton",
+  TITLE="{The Pizza.py toolkit}",
+  HOWPUBLISHED={\url{http://www.cs.sandia.gov/~sjplimp/pizza.html}}
+}
+
+
+@ARTICLE{TraPPE,
+  AUTHOR="Marcus G. Martin and J. Ilja Siepmann",
+  TITLE="Transferable Potentials for Phase Equilibria. 1. United-Atom Description of n-Alkanes",
+  JOURNAL="J. Phys. Chem. B",
+  VOLUME=102,
+  NUMBER=14,
+  PAGES={2569--2577},
+  YEAR=1998
+}
+
+
+@ARTICLE{Raviv++SafinyaBiophysJ2007,
+   AUTHOR="Uri Raviv and Toan Nguyen and Rouzbeh Ghafouri and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Robijn F. Bruinsma and Cyrus R. Safinya",
+   TITLE="Microtubule Protofilament Number Is Modulated in a Stepwise Fashion by the Charge Density of an Enveloping Layer",
+   JOURNAL="Biophys. J.",
+   VOLUME=92,
+   NUMBER=1,
+   PAGES={278--287},
+   YEAR="2007",
+   MONTH={January},
+   DAY={1}
+}
+
+
+@ARTICLE{Raviv++SafinyaPNAS2005,
+   AUTHOR="Uri Raviv and Daniel J. Needleman and Youli Li and Herbert P. Miller and Leslie Wilson and Cyrus R. Safinya",
+   TITLE="Cationic liposome-microtubule complexes: Pathways to the formation of two-state lipid-protein nanotubes with open or closed ends",
+   JOURNAL="Proc. Natl. Acad. Sci. USA",
+   VOLUME=102,
+   NUMBER=32,
+   PAGES={11167--11172},
+   YEAR="2005",
+   MONTH={August},
+   DAY={9}
+}
+
+@ARTICLE{Berendsen++StraatsmaJPhysChem1987,
+   AUTHOR="H. J. C. Berendsen and J. R. Grigera and T. P. Straatsma",
+   TITLE="The Missing Term in Effective Pair Potentials",
+   JOURNAL="J. Phys. Chem.",
+   VOLUME=91,
+   NUMBER=24,
+   PAGES={6269--6271},
+   YEAR="1987",
+}
+
+
+@ARTICLE{Klimov+ThirumalaiPRL1997,
+   AUTHOR="Klimov, D. K. and Thirumalai, D.",
+   JOURNAL="Phys. Rev. Lett.",
+   VOLUME=79,
+   PAGES={317--320},
+   YEAR="1997"
+}