Open source molecular dynamics analysis tools for GROMACS
Open source molecular dynamics analysis tools for GROMACS
I am a doctoral candidate in chemical engineering at the University of Louisville. Prior to starting the Ph.D. work I had practiced as a control systems engineer in the petrochemical industry for over 30 years. I have professional engineering licenses in chemical (1985) and electrical (1988) engineering. I will graduate May 9, 2020.
Primarily my research is simulation of biophysical processes related to membranes, membrane proteins and the role of the electric field in establishing equilibrium membrane/protein structures and the modulation of membrane protein channel transport.
The use and explanation of the two files above are explained in the paper “Insights into the molecular mechanisms of electroporation from computational electrophysiology”, in Biophysical Journal.
The rest of the scripts in this repository here take the trajectory files produced by the select. and shift. scripts and do additional processing to center the biostructure of interest in every frame. The resulting “centered” trajectories can then be processed to map the non-uniform electric flux and to produce data files we call Computational X-Rays. Files to describe the methods of implementation and figures resulting from the analysis will also be posted.