From 3f33d2af1916f16665f903c6b1d74d44d73e1027 Mon Sep 17 00:00:00 2001 From: Avimanyu Bandyopadhyay Date: Sun, 6 May 2018 10:53:18 +0530 Subject: [PATCH] Delete paper.md --- paper.md | 67 -------------------------------------------------------- 1 file changed, 67 deletions(-) delete mode 100644 paper.md diff --git a/paper.md b/paper.md deleted file mode 100644 index 31ddd05..0000000 --- a/paper.md +++ /dev/null @@ -1,67 +0,0 @@ ---- -title: 'TrajectoryMergeAssist: A Python based tool to simplify extended molecular dynamics simulations on Desmond' -tags: - - Python - - Desmond - - Bioinformatics - - Trajectories - - Molecular Dynamics - - Extended Simulations -authors: - - name: Avimanyu Bandyopadhyay - orcid: 0000-0003-4806-2238 - affiliation: 1 -affiliations: -- name: Bioinformatics Lab, Dept. of Biotechnology, Heritage Institute of Technology, Kolkata, India - index: 1 - -date: 03 May 2018 -bibliography: paper.bib ---- - -# Summary - -Working with trajectories[@Robert2015MDTraj] generated with the Desmond molecular dynamics -software[@Kevin2006Scalable] 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[@Desmond], 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[@Maestro]. ``TrajectoryMergeAssist`` also takes care of this by generating an "-out.cms" file -instead of ".cms". - -## Usage Links - -1. [Repository](https://github.com/avimanyu786/TrajectoryMergeAssist) - -2. [Releases](https://github.com/avimanyu786/TrajectoryMergeAssist/releases) - -3. [Documentation](https://github.com/avimanyu786/TrajectoryMergeAssist/wiki) - -# References