About This is code for analyzing the xtc file used in GROMACS, a molecular dynamics simulation program.
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Updated
Nov 13, 2023 - Python
About This is code for analyzing the xtc file used in GROMACS, a molecular dynamics simulation program.
This is a tool to generate GROMACS input files using the SAFT-gamma Mie forcefield. The input files contain all information except the angle and torsion potentials, so add accordingly.
Part of the diploma.
GroDecoder extracts and identifies the molecular components of a structure file (PDB or GRO) issued from a molecular dynamics simulation.
This is code for analyzing the gro/xtc file used in GROMACS, a molecular dynamics simulation program.
A molecular dynamics approach to study the permeation of nanoparticles through lipid bilayer
Analysis postprocessing utilities for my molecular dynamics simulations of LiTFSI-Ether mixtures
A collection of scripts and software to assist with biomolecular simulation in our laboratory
Create a consistent, documented pipline and folder structure for self-consistent MD charge optimization.
Adjust coordinates and virtual sites for use with various water models in gromacs
Alternative to the native gmx saltbr Gromacs function for estimating the occurance of salt bridges in peptides and proteins over a simlation trajectory
A tool to analyse the distribution of water molecules in the first solvation shell of certain molecules.
G96 format based reporter for OpenMM
A Tinker Trajectory Converter
Generation and visualization of 3d protein sequences
A development version of GROMACS with extra feature branches by Molecular Biomechanics (MBM) group at HITS.
A tool to detect nanobubbles formed in MD simulations.
Shell scripts to run and extract output from GROMACS benchmarks.
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