piskuliche Goto Github PK

average-calc

Calculates block averages of a data file.

cassandra_batch_input

A python program for

chem-852

Chem852 Programming Assignments

contact-analysis

This is a code for calculating contacts within a certain range of distances from simulations in GROMACS.

direct_calculation_fluctuations

This is a code to calculate activation energies and activation volume using the methods described in Piskulich, Mesele and Thompson, "Removing the Barrier to the Calculation of Activation Energies: Diffusion and Reorientation in Liquid Water", J. Chem. Phys., 2017

electric_field_cell_list

Cell-list decomposition approach to calculating the electric field for computational spectroscopy.

empiricalmapping

This is a code for generating empirical maps from molecular dynamics simulations (and electronic structure calculations).

energy-fluctuations

A series of codes for calculating the activation energy of diffusion of a molecule.

fortran-distance-module

A fortran module for calculating distances between coordinates (within a cutoff)

gaussian-utilities

A small collection of python codes for analyzing gaussian calculations. Use at your own risk.

generalized-replica-exchange

A python wrapper for setting up, running, and analyzing gREM simulations with LAMMPS.

githubgraduation-2021

Join the GitHub Graduation Yearbook and "walk the stage" on June 5.

githubworkshop

This is for a github workshop

h-bond-analysis

h-bond-distributions

A general program for identifying and histogramming Hydrogen Bond Distributions.

hydrogen-bonding

A module for calculating hydrogen bonds from MD simulations

hydrogen_bond_statistics

ihpcss-programming-challenge-2023

input_examples

A place where I can place input examples for various programs and software to share with others.

itp2moltemplate

Python script for converting Martini ITP files to moltemplate force field files.

itp_2_hoomd

[Work in Progress] A set of python programs to convert a gromacs ITP style (in the OPLS AA format) to a HOOMD simulation.

jumpshell

lammps

Public development project of the LAMMPS MD software package

libgmxfort

Modern Fortran toolkit for analyzing GROMACS simulations

libxdrfile

Fork of library used in reading xtc files from GROMACS simulations

lipid-phase-ml

This is a code that calls the MLLPA software and does ML to figure out lipid phases.

local-liquid-structure

C++ Code to calculate the radial distribution function, g(r)

molecular-volume-montecarlo

Uses a Monte Carlo based approach to calculate the actual volume of a molecule.

multiplemoleculetransport

Initial Build

my-code-collection

A repository to store a variety of codes