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amyloid-simulations

Various simulations of coarse-grained amyloid models using the lammps_multistate_rods library

blogs

codinginterviews2-bypython

此项目是《剑指offer》第二版里算法面试题的Python3实现版本，作为一本经典书籍，可以时常拿出来看一看、翻一翻、记一记。同时也是为了Python程序员能够更好的通过公司的技术面试，拿到心仪的offer。

corrections

Corrections to the text of the book "Computer Simulation of Liquids" by Michael P. Allen and Dominic J. Tildesley (2nd edition, Oxford University Press, 2017)

cs224w_gnn

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.

dendrimer-builder-toolkit-dbt-_8multiplicity

Dendrimer Builder Toolkit (DBT) with maximum of 8 multiplicity

dmd_trj2gro

ebdims

Core scripts to run eBDIMS protein dynamics transitions

enhanced_sampling_methods_tutorials

Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..

esp_ex2

A python script to read the cub file of electrostatic potential calculated by Gaussian and extract the electrostatic potentials at 0.001 a.u.

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.

fep-benchmark

Benchmark set for relative free energy calculations.

flask

python flask web

fluxer

A script for counting crossing events across a finite width xy-plane membrane.

fortran.tmbundle

TextMate support for Fortran

g_mmpbsa

MM-PBSA method for GROMACS. For full description, please visit homepage:

gervasio-protein-dynamics

A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery

gmx_makecyclictop

This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology file

gopy

gromacs-fda

Force Distribution Analysis (FDA) for GROMACS

gromacswrapper

GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools (v4.6.x, v5.x, 2016.x, 2018.x, 2019.x, all with the same Python code) into python scripts.

hdz-dox-parameters

huangjianxiangzju.github.io

ic50

a very simple fitting script to calculate IC50

indus

Implements the INDUS method for several probe volume geometries.

kinesin

Kinesin

lammps_multistate_rods

A python library for simulating rod-like structures with multiple states (conformations) in LAMMPS.

leapfrogmdpython

A simple (toy) MD code implemented in Python

liposome-membrane-thickness