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


Keywords
simulation, LAMMPS, molecule editor, molecule builder, ESPResSo, amber, coarse-grained-molecular-dynamics, compass, force-fields, martini, molecular-dynamics, molecule-builder, molecule-editor, opls, sdk
License
BSD-3-Clause
Install
pip install moltemplate==2.10.13

Documentation

Build Status License

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 . --user

This will install moltemplate for a single user. On a shared computer, to install moltemplate system-wide, use:

sudo pip install .

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
python3 -m venv venv     #(or "virtualenv venv" if using python2)
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. Virtual environments are explained 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. I recommend installing virtualbox in windows together with a (debian-based) linux distribution with a lightweight desktop such as xubuntu. Alternatively, if you are using Windows 10 or later, you can try installing the "Windows Subsystem for Linux (WSL)", as explained here and here, or Hyper-V. Otherwise, if you are using an older version of windows, try installing CYGWIN instead.

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. If you are NOT using WSL, then you can also use a graphical text editor which might be easier for a beginner to use. Such editors include Atom, Sublime, Notepad++, VSCode, and the graphical versione of emacs and vim. (Don't use these editors to edit files within the WSL environment.)

License

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