Scratchings on biomolecular simulation and theory

George A. Pantelopulos

I am a post-doctoral scholar working under the supervision of Robert Best and the Laboratory of Chemical Physics at NIH/NIDDK.

I recently completed my PhD with John E. Straub of the Boston University Chemistry Department. My new focus is on modeling of collagen and the extracellular matrix with atomistic accuracy with a focus toward reproduction of multiscale mechanics. This website is used to occasionally catalogue write-ups on theory, analysis, and software for sharing with colleagues.

Generic LJ Simulator in OpenMM

14 minute read

I present a script and JSON input file for building and running complex Lennard-Jones particle mixtures in 2D and 3D in a variety of conditions using OpenMM.

Implicit Membrane REMD Structures of Full-length C99 protein

5 minute read

I briefly discuss preparation of full-length C99 simulations in GBSW implicit membranes using REMD and provide prepresentative structures from clustering.

Lipid Bilayer Phase Diagrams and Phase Diagram Evaluation Methods

less than 1 minute read

I post some notes I wrote about ternary lipid bilayer phase diagrams and phase diagram sampling methods.

How to Determine When a Lipid Bilayer is Phase Separated

6 minute read

I discuss the definition of lipid miscibility point used in experiment and determine the equivalent size-depedndent binary mixing entropy for a 2D lattice.

Lipid Mixing Entropy with Voronoi Tessellation

3 minute read

I discuss mixing entropy as an order parameter for lipid mixing and describe a Voronoi tessellation-based method and calculation using MDAnalysis and scipy.