amberMDgui
Linux software pipeline for Amber molecular dynamics simulation
DOWNLOAD .tar.gz DOWNLOAD .zip AMBER INSTALLER .zipUser README file
A descriptive general README for concept, implementation advice and troubleshooting
Link to PDF
DROIDS 4.0
amberMDgui is an extension of our long term DROIDS software project for comparative molecular dynamics
Link to website
The G.A.Babbitt Lab at the Rochester Institute of Technology
Our research
Our research is focused upon gaining a better understanding of how the biophysical function of proteins, DNA and other molecules constrains molecular evolution. We employ a computational approach, taking advantage of many methods in computer simulation, machine learning, statistics and traditional bioinformatics. We are working closely Dr. Ernest Fokoue's research group to develop machine learning applications to molecular dynamics.
Our group
Our research group consists of primarily undergraduate students working in many programs across RIT, including Biomedical Engineering, Biotechnology, Biology, Computer Science, Math and Bioinformatics. Most students work for the lab on a volunteer basis, with very flexible schedules, working towards publishable projects that can be added to a students' resume.
How to join our group?
Students interested in working with the lab should contact me at gabsbi(at)rit.edu. Volunteers should have some proficiency in either computer programming, mathematics and/or molecular biology and be willing to commit about a year of their spare time towards the goals of the group.
If you publish your results...
amberMDgui is a part of our DROIDS 4.0 project. To cite DROIDS, please see the links below
first citation - Biophysical Journal second citation - Biophysical Journal third citation - bioRxiv preprintpublished example from our lab
Gregory A. Babbitt , Miranda L. Lynch , Matthew McCoy , Ernest P. Fokoue & André O. Hudson (2020): Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2020.1815578
PDF - JBSDOperating System Requirements
This was is tested upon Linux Mint 18/19 with Amber 16/18 and OpenMM. Amber only runs on Linux. Any Debian desktop OS (e.g. Ubuntu) should work. We prefer Linux Mint because its Driver Manager greatly eases the management of Nvidia graphics drivers during initial system build. See also our instructions for running Virtual Machines on Windows and Google Cloud.
Graphics Processor Requirements
Nvidia GTX 1080, RTX 2080 or Titan X are recommended. DROIDS can utilize systems with single GPU, dual independent GPUs, or multiple GPUs connected by SLI. NOTE: Amber requires additional testing on SLI stacks. Nvidia GPU enabled Ubuntu Linux Virtual Machines instances are very easy to build on the Google Cloud Platform.
Licensing
Our work is freely distributed under GPL3 license. GPU accelerated Amber 18 is licensed under Univ of CA. See the Amber homepage for purchase details (https://ambermd.org/). Alternatively, the open source OpenMM python library can be used.
Major Software Dependencies
Nvidia CUDA 9.0 and CUDA Dev tools, MD software = Amber16/18(licensed) or OpenMM (open source), R software, UCSF Chimera software for molecular visualization.
Amber Installation
We supply a flexible installer script (perl AMBERinstaller.pl) with the main tar.gz file. It will install CUDA, Amber, Ambertools, OpenMM and all other dependencies.