TrajectoryMergeAssist: A Python based utility to simplify extended molecular dynamics simulations on Desmond

Bioinformatics Lab, Dept. of Biotechnology, Heritage Institute of Technology, Kolkata, India

Summary

Working with trajectories generated with the Desmond molecular dynamics
software can become quite inconvenient when simulations are extended
multiple number of times with the same. Extended simulations allow Bioinformaticians to observe
and interpret plots upto greater lengths of time and also do it at their own time of convenience
when with lesser resources.

To make this process simpler and easier, TrajectoryMergeAssist was created.
It is a very handy and user-friendly GUI tool for Bioinformaticians to manage extended
trajectories and finally merge all of them into a single trajectory with a series of
steps and observations:

With every gradual extended simulation, the user would like to view the resultant plots
starting from the first trajectory until the end of the second. The user would be eager
to view the resultant RMSD/RMSF plot of the same after the end of each extended simulation
and that is when this tool becomes very useful. With further extended simulations, the user
can use the combined trajectory obtained previously and merge it with the third and so on.

The tool has been written in Python 2.7 and makes use of Tkinter, one of Python's own GUI
programming toolkits. Another version has also been written in Python 3.

Key Features

Works with both the latest and older versions of Desmond

Starting with Desmond 2018.1, a new Desmond script has been introduced and the earlier
one has been deprecated for merging trajectories. TrajectoryMergeAssist checks for the same
and proceeds accordingly, in order to support both the latest and earlier versions.

Generates "-out.cms" file ready for use in Maestro

Unlike versions prior to 2018.1, Desmond creates "merged.cms" files instead of "merged-out.cms",
making it a requirement to manually rename it to the latter to make it ready for viewing on
Maestro. TrajectoryMergeAssist also takes care of this by generating an "-out.cms" file
instead of ".cms".

Usage

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

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

Steps to use TrajectoryMergeAssist

1. The "TMA.py" or "TMA_PY3.py" file has to be present in a directory containing 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:

    python TMA.py
    
    or
        
    python3 TMA_PY3.py      -- 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

References

Robert T. McGibbon, Matthew P. Harrigan, Kyle A. Beauchamp. 2015. “MDTraj: A
Modern Open Library for the Analysis of Molecular Dynamics Trajectories.” Biophysical
Journal 109 (October). Elsevier:1528–32. https://doi.org/10.1016/j.bpj.2015.08.015.

Kevin J. Bowers, Huafeng Xu, Edmond Chow. 2006. “Scalable Algorithms for Molecular
Dynamics Simulations on Commodity Clusters.” In Proceedings of the 2006 Acm/Ieee
Conference on Supercomputing. SC ’06. Tampa, Florida, USA: CiteSeerx. https://
citeseerx.ist.psu.edu/viewdoc/citations;jsessionid=7C3245078BA824BB27F36C8A726A576F?
doi=10.1.1.98.2121.

D. E. Shaw Research, New York, LLC. n.d. “D. E. Shaw Research | Desmond.” https:
//www.deshawresearch.com/resources_desmond.html.

Schrödinger, New York, LLC. n.d. “Schrödinger | Maestro.” https://www.schrodinger.
com/maestro.