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Welcome to the TrajectoryMergeAssist wiki!

Easy Installer

Download the installer.

To install, just use a terminal and run:

chmod +x tma_v2.1-setup.sh

./tma_v2.1-setup.sh

tma-setup.sh will also set the path for you.

Run TrajectoryMergeAssist GUI with the following simple command:

tma

Supported Linux Distros for the installer: Debian based, CentOS, Fedora and RHEL

Manual Installation

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 and all prerequisites, proceed as follows:

1. Open a Terminal.

2. Download tma_v1.2.tar.gz from Releases:

   wget https://github.com/avimanyu786/TrajectoryMergeAssist/releases/download/v1.2/tma_v1.2.tar.gz

3. Extract the tarball package:

   tar -xvzf tma_v1.2.tar.gz

4. Your destination location{installation home} is now /home/{username}/tma_v1.2

5. 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.

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

   Create a new environment variable:

   $TMAPATH=/home/{username}/tma_v1.2/bin

6. Restart your Linux session.

7. Now you can start TrajectoryMergeAssist from any directory containing input data.

   Launch a terminal and run TrajectoryMergeAssist GUI with the following simple command:

   tma

Steps to use TrajectoryMergeAssist

i. Merging Desmond MD trajectories

1. Make sure you have the following required input files and trajectories:

   a. The "-out.cms" file

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

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

2. It is 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 trajectory directories ending with "_trj"

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

7. Click on "Merge Desmond 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

ii. Merging GROMACS MD trajectories

1. Make sure you have the following required input files and trajectories:

   a. The first trajectory file (name ends with ".xtc")

   b. The second trajectory file from an extended GROMACS MD simulation

2. It is 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. Choose the two trajectory files ending with ".xtc"

5. The 2 choices will be visible in the background terminal so that the selections can be confirmed.

6. Click on "Merge GROMACS Trajectories"

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

8. The new merged trajectory (".xtc" file) can be found in the same working directory.

Optional Step

If you have more than two trajectories, use the new merged trajectory to merge with the 3rd and so on.