Discontinuous Molecular Dynamics (DMD) Simulation Package
☆16Jun 8, 2026Updated last week
Alternatives and similar repositories for sDMD
Users that are interested in sDMD are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- This software package simulates the reduction of graphene oxide and calculates the optical response of the generated sp2 domains☆11Dec 22, 2016Updated 9 years ago
- PiViewer: an open-source tool for automated detection and display of pi-pi interactions☆14Jun 6, 2018Updated 8 years ago
- An event-driven particle simulator and visualisation code. Please see the website below for more information.☆60Aug 13, 2025Updated 10 months ago
- A force field for the simulation of inorganic-organic interfaces (INTERFACE-CHARMM, INTERFACE-PCFF)☆23Feb 14, 2024Updated 2 years ago
- Supernova's MM-PBSA binding free energy calculation tool.☆12Updated this week
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆15Nov 24, 2020Updated 5 years ago
- COSMO: COarse-grained Simulation of intrinsically disordered prOteins with openMM☆15Jun 10, 2026Updated last week
- Convenience functions for VMD-TCL scripting☆14Apr 3, 2026Updated 2 months ago
- reactive MD python pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)☆14Nov 19, 2019Updated 6 years ago
- Automatic CHARMM-GUI browser interaction with Python☆19Mar 20, 2023Updated 3 years ago
- ☆21Jul 16, 2020Updated 5 years ago
- A python implementation of the string method with swarms of trajectories using GROMACS☆19Oct 19, 2022Updated 3 years ago
- Xlink is a Python script that uses Gromacs to automatically perfom simulation crosslinking and generate atomistic model of aromatic polya…☆17Jul 8, 2023Updated 2 years ago
- Package for reading, analysis and visualization of metadynamics HILLS☆40Nov 28, 2023Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Get Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- Reactive MD pipeline for GROMACS using Kinetic Monte Carlo / Molecular Dynamics (KIMMDY)☆22Apr 27, 2026Updated last month
- Computation of the drug-target relative residence times from RAMD simulations☆23Aug 29, 2024Updated last year
- ☆22Jul 14, 2022Updated 3 years ago
- Coarse-grained mapping and parametrisation for the Martini 3 forcefield☆23May 27, 2026Updated 3 weeks ago
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆17Jun 8, 2026Updated last week
- This package is meant to calculate the dihedral entropy of a biomolecule. However, it can also calculate the entropy of any binnable dat…☆24Feb 2, 2024Updated 2 years ago
- A Python library for constructing polymer topologies and coordinates☆22Sep 23, 2025Updated 8 months ago
- Implementation of methods to sample from Boltzmann distributions☆22Jan 24, 2023Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 3 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46May 3, 2021Updated 5 years ago
- Flexible storage of chemical topology for molecular simulation☆70Jun 9, 2026Updated last week
- Gromacs topology template generator☆16Jul 15, 2021Updated 4 years ago
- An implementation of the AWSEM coarse-grained protein folding forcefield in OpenMM☆38May 28, 2025Updated last year
- Python interface for Enhanced Monte Carlo (EMC)☆23Apr 27, 2026Updated last month
- TS2CG version 2☆27Apr 18, 2026Updated 2 months ago
- Automatic generation of LAMMPS data file for atomistic and coarse-grained simulations of molecular and polymeric materials with various t…☆24Mar 24, 2026Updated 2 months ago
- Perform polymerization and crosslinking in MARTINI coarse-grained forcefield using GROMACS MD package☆29Jan 21, 2026Updated 4 months ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- A simple implementation of replica exchange MD simulations for OpenMM.☆26Jul 19, 2021Updated 4 years ago
- Associative memory, Water mediated, Structure and Energy Model (AWSEM) protein simulation code☆41Dec 11, 2025Updated 6 months ago
- ☆13Mar 26, 2024Updated 2 years ago
- GridMAT-MD membrane analysis program☆26Sep 15, 2018Updated 7 years ago
- A collection of heat engines, based on the OpenAI Gym environment framework for use with reinforcement learning applications.☆15Dec 20, 2021Updated 4 years ago
- Predicting the effect of mutations on protein stability using a simple orientational potential.☆20Jul 5, 2024Updated last year
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆27Jun 8, 2024Updated 2 years ago