Dec 16, 2015

How to use Moltemplate on Windows OS systems

Moltemplate (http://www.moltemplate.org/) is a powerful tool for configuring molecules and assigning force field parameters.
However, its use on Windows OS is somewhat tricky.

1. Install Cygwin (https://cygwin.com/install.html).  Installation of required packages + python should be good enough.

2. Copy all Moltemplate files to C:\cygwin64\home\moltemplate

3. Open "C:\cygwin64\home\username\.bash_profile" in a text editor.  Add a new PATH (in yellow) to a section "# Set PATH so it includes user's private bin if it exists".  For example,

# Set PATH so it includes user's private bin if it exists
# if [ -d "${HOME}/bin" ] ; then
   PATH="/bin/:/home/moltemplate/"
# fi

In Cygwin console (terminal), we can check if the PATH is correctly set by typing "echo $PATH"

5. Place examples (http://www.moltemplate.org/) in C:\cygwin64\home\moltemplate\examples

6. In Cygwin command window (console or teminal), navigate an example folder
(e.g., cd /home/moltemplate/examples/all_atom_examples/force_field_explicit/waterSPCE+Na+Cl/moltemplate_files)

7. In Cygwin command window, type:

moltemplate.sh  -atomstyle "full"  system.lt
or
moltemplate.sh  -xyz  system.xyz  -atomstyle "full"  system.lt
(This will use a premade xyz configuration of system, e.g., system.xyz).

LAMMPS input and data files will be created.  (e.g., system.in and system.data)

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