Xiaoliang1127

TWRA_HALF_CAGE

topological method for identification of hydrate cages

MDLAMMPS

parses lammps trajectory files to get densities along the z-axis

MDBrushAnalysis

Library of Python classes for parsing LAMMPS density profiles and data files, and specifically for post-processing of MD simulations of polymer brushes in equilibrium with solvent vapours.

LAMMPyS

Python tools for LAMMPS calculation pre- and post- data processing. (Based on pandas datafram)

psiphon

Meta-repo with info about and links to Psiphon resources

Website

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10.1021-acs.langmuir.0c01949

Progressive Molecular Rearrangement and Heat Generation of Amorphous Polyethene Under Sliding Friction: Insight from the United-Atom Molecular Dynamics Simulations

lammps

create lammps model data file code

Lammps-to-PDB-writer

This code converts LAMMPS data files to PDB files. Much of the information in the files is mostly filler, but they contain coordinate information as well as atomic symbols and weights.

pdb-tool

This is a tool for editing files downloaded from Protein Data Bank (PDB)

topobuilder

a py script which helps build topology file for LAMMPS from *.pdb (currently only available for CHARMM-gen ff)

cif2cell-lammps

pizza

Pizza.py is a loosely integrated collection of tools written in Python, many of which provide pre- and post-processing capability for the LAMMPS molecular dynamics package.

lammps-data-file

[UNMAINTAINED] Lammps data file creation

vmd_hbonds

hbonding_analysis

hbonds

hbond

HBonds

identifying atoms capable of h bonding

hbond

halogen bonding

HBondIdentifier

A small program helps finding water bridge in pdb files, written in fortran. Please note that it's a first usable version, and only support CHARMM-formatted PDB file.

HbondTwister

Recognising hydrogen bonds based on geometric constraints and creating rotation poses along the h-bond axis.

hbond

TraceHBonds

Find strings of hydrogen bonded atoms in a trajectory file.

hbonds

hbond_analysis

hbonding for residue pairs

pdb2lmp

Convert PDB files to LAMMPS data and force field files.