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Avimanyu Bandyopadhyay edited this page Sep 13, 2018 · 33 revisions

Welcome to the TrajectoryMergeAssist wiki!

Prerequisites

To be able to use the tool, the python-tk or tkinter package would be required in addition to Python on Linux.

Please sure you have the path to Desmond configured correctly (in general, it looks like $SCHRODINGER=/opt/schrodinger2018-3). You can refer to this guide to make sure the path to Desmond is set correctly.

For systems like Ubuntu, Tkinter can be installed with a Linux terminal online by the following command:

sudo apt-get install python-tk

For Python3 on Ubuntu, the terminal command would be:

sudo apt-get install python3-tk

For CentOS type systems, the installation can be done via:

sudo yum install tkinter

For Python3 on CentOS, the preferable command would be:

sudo yum install python34-tkinter

or

sudo yum install python36u-tkinter

Installing on Linux

Assuming you have Desmond installed with its default path set correctly.

  1. Open a Terminal.

  2. Download TrajectoryMergeAssist_v1.1.03.tar.gz from Releases:

    wget https://github.com/avimanyu786/TrajectoryMergeAssist/releases/download/v1.1.03/TrajectoryMergeAssist_v1.1.03.tar.gz

  3. Extract the tarball package:

    tar -xvzf TrajectoryMergeAssist_v1.1.03.tar.gz

  4. Your destination location{installation home} is now /home/{username}/TrajectoryMergeAssist_v1.1.03

  5. Add {installation home}/bin to your PATH environment variable by adding a ":".

    Create a new environment variable:

    $TMAPATH=/home/{username}/TrajectoryMergeAssist_v1.1.03/bin

    On Ubuntu 14.04 and 16.04, we have tested it by using the /etc/environment variable for this step.

    It is recommended you do a backup of the same before making any changes.

    Now you can start TrajectoryMergeAssist from any directory.

  6. Restart your Linux session.

  7. Now you can launch a terminal and run TrajectoryMergeAssist GUI with the following simple command:

    tma

How to use TrajectoryMergeAssist (TMA)

  1. Make sure the directory from where you start TMA contains the following required input files and trajectories:

    a. The "-out.cms" file

    b. The first trajectory directory(ends with "_trj")

    c. The second trajectory directory from an extended Desmond MD simulation.

  2. It is strongly recommended to work with the above files from a location like:

    /home/username/directory/

  3. Navigate to the directory on a terminal window and run:

    tma

    or

    tma-py3 -- For Python3 Only

  4. Select the "-out.cms" file

  5. Navigate to the two "_trj" directories

  6. The 3 choices will be visible in the background terminal so that the selections can be confirmed.

  7. Click on "Merge Trajectories"

  8. Wait until the "...Done!" message

  9. The new merged trajectory along-with the new "-out.cms" file can be found in the same working directory.

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