Guideline for Using Moltemplate in Windows

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Dear all windows users:

Just want to share my experience of using moltemplate in windows:

  1. Download Cygwin : https://cygwin.com/install.html

Follow those (http://stackoverflow.com/questions/21230657/what-is-the-current-full-install-size-of-cygwin; http://x.cygwin.com/docs/ug/setup-cygwin-x-installing.html) to choose the package of Cygwin.

I installed the full package of Cygwin.

If you choose to install the full package, you may not complete the download at once. You can resume the installation by reopening
the install file (for example : setup-x86.exe), and following the guideline and keep all thing same as previous (the mirror site, the directory),
it will pick up where you disconnected.

  1. Download Moltemplate (http://www.moltemplate.org/downloads/moltemplate_2014-5-19.tar.gz)

After unzipping, put the moltemplate folder (moltemplate_2014_5_19) in the home directory of Cygwin(~\cygwin64\home)
and change the folder name to moltemplate ( the original folder contains date)

  1. Go ~\cygwin64\etc\defaults\etc\skel to look for .profile, .bash_profile, .bashrc files

If you have all of those, open and read each files’ comments and put two lines:

export PATH="$PATH:$HOME/moltemplate/src"
export MOLTEMPLATE_PATH="$HOME/moltemplate/common"

in one of those files

I have .profile, .bash_profile , .bashrc, .inputrc and I put the above two lines in bash_profile as in the .profile it said:

This file is not read by bash(1) if ~/.bash_profile or ~/.bash_login exists.

if running bash

if [ -n “{BASH_VERSION}" ]; then if [ -f "{HOME}/.bashrc” ]; then
source “${HOME}/.bashrc”
fi
fi

The way to open those files (.profile etc):
a. windows notepad
b. notepad ++ (very powerful, http://notepad-plus-plus.org/)

  1. Download the example (first three files) Aggregation of Simple Toy Polymers from http://www.moltemplate.org/, put them in the moltemplate folder

, use Cygwin navigate to the folder and type moltemplate.sh -atomstyle “full” system.lt in Cygwin command window.

Magic happens [make sure you already have Python installed]

  1. Download VMD and TOPOTOOLS (https://sites.google.com/site/akohlmey/software/topotools)

Put the files in topotools floder into the VMD folder( ~\Program Files (x86)\University of Illinois\VMD)

In the VMD command window, type topo readlammpsdata system.data full

Version information:

a. VMD 1.9.1
b. TOPOTOOLS 1.4

Best Wishes!