dstelter92 / moltemplate

A general cross-platform text-based molecule builder for LAMMPS

Moltemplate

Description

Moltemplate is a general cross-platform text-based molecule builder for LAMMPS and ESPResSo. Moltemplate was intended for building custom coarse-grained molecular models, but it can be used to prepare realistic all-atom simulations as well. It currently supports the OPLS, COMPASS, AMBER(GAFF,GAFF2), MARTINI, SDK, LOPLS(2015), EFF, and TraPPE(1998) force fields, numerous solvent models, and includes approximately 40 examples. (New force fields and examples are added continually by users.)

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     #(or "python3 -m venv venv" if using python3)
source venv/bin/activate
pip install .       #(or "pip3 install ." if using python3)
#(now do something useful with moltemplate...)

(You will have to "run source ~/moltemplate/venv/bin/activate" beforehand every time you want to run moltemplate. The virtualenv tool is explained in detail here) 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.)

License

Moltemplate is available under the terms of the open-source 3-clause BSD license. (See "LICENSE.md")