jrdcasa Goto Github PK

allen-tildesley-data

Data files which may be used to test examples accompanying the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Clone or download" button, or follow the "...releases" link below.

allen-tildesley-examples

Fortran and Python examples to accompany the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017). Use the "Clone or download" button, or follow the "...releases" link below.

bunch_materialsstudioscripts

chiripa

Chiripa: CHI interRaction PArameter

conky_configuration

Conky configuration files in my SLIMBOOK laptop

dcdfort

Modern Fortran toolkit for reading in and analyzing DCD simulation trajectories output from LAMMPS

foyer_cj

A copy of the package foyer (A package for atom-typing as well as applying and disseminating forcefields foyer.mosdef.org)

gecos

Generation of conformers

gecos2

GeCoS: A toolkit to generate conformers and calculate properties derivate from ab-initio calculations

gecos_streamlit

gmso_cj

handlegaussian

Disaccharides Alba

intermol_cj

InterMol: a conversion tool for molecular dynamics simulations. I have added the possibility to use Toxvaerd potentials for *-CH2-CH2-* in GROMACS and LAMMPS ( Toxvaerd, S. J. Chem. Phys. 1997, 107, 5197). This potential is important for polyethylene segments improving the dimension chains respect to TrappeUA

jrdcasa

Config files for my GitHub profile.

k_fit_cj

An algebraic approach to determine the torsional coefficients

libgmxfort

Modern Fortran toolkit for analyzing GROMACS simulations

libxdrfile

Fork of library used in reading xtc files from GROMACS simulations

matstudio-workflows

A collection of scripts that automate computational chemistry calculations within Materials Studio.

mbuild

A hierarchical, component based molecule builder

opls-aam

Implementing OPLS-AA/M Force field in OpenMM from CHARMM formatted parameter files

opls-aam_for_gromacs

Gromacs Implementation of OPLS-AAM Force field

oplsaa-db

Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.

passwd-encrypt

This is a simple package to encrypt and decrypt strings using RSA keys.

polyanagro

Python toolkit to analyze molecular dynamics simulations.

polymernen

Normalizing polymer named entities

pycgmappol

Mapping AA to CG models

pysimm

python simulation interface for molecular modeling

qforce_jrd

Q-Force is a software package for deriving all-atom force fields from quantum mechanical calculations in an automated manner

replicate_polymer_topology

Replicate polymer topology based on topology library. A toolkit to extend and type polymer systems

sphinx-gui3

This is a simple editor for Markdown and reStructuredTest (rst) markup languages with Sphinx and Rst2Pdf support