A python implementation of the string method with swarms of trajectories using GROMACS
☆19Oct 19, 2022Updated 3 years ago
Alternatives and similar repositories for string-method-swarms-trajectories
Users that are interested in string-method-swarms-trajectories are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Supporting data for the manuscript "Deep learning the slow modes for rare events sampling"☆23Jun 6, 2024Updated 2 years ago
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated 10 months ago
- ☆22Dec 15, 2022Updated 3 years ago
- Python implementation of Dynamical Network Analysis☆16Aug 6, 2025Updated 11 months ago
- ☆13Feb 18, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Mar 7, 2025Updated last year
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆17Updated this week
- Rethinking Metadynamics: From Bias Potentials to Probability Distributions☆15Sep 18, 2023Updated 2 years ago
- A VMD molfile plugin reader for HOOMD-blue GSD files.☆21Jul 6, 2026Updated 2 weeks ago
- HOOMD-blue example scripts.☆39Updated this week
- SIEVE-Score: interaction energy-based virtual screening method based on random forest.☆14Sep 15, 2023Updated 2 years ago
- Discontinuous Molecular Dynamics (DMD) Simulation Package☆16Jun 8, 2026Updated last month
- DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces☆18May 7, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Cryptic pocket prediction using AlphaFold 2☆25Nov 27, 2022Updated 3 years ago
- An efficient, multithreaded weighted histogram analysis (WHAM) implementation for the post-processing of umbrella MD simulations.☆29Apr 1, 2024Updated 2 years ago
- A TCL code for the calculation of mass/number density of a system.☆19Jun 21, 2024Updated 2 years ago
- GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the …☆12Apr 7, 2023Updated 3 years ago
- some generic (but hopefully still useful) recommendations on writing your thesis☆11Mar 24, 2023Updated 3 years ago
- MM and QM/MM setup for a metalloprotein using GROMACS, Chemshell and ORCA (Using the CHARMM forcefield (both in GROMACS and with Chemshe…☆28Jun 8, 2024Updated 2 years ago
- ☆24May 8, 2026Updated 2 months ago
- Free Energy Landscape analysis tool.☆32Feb 15, 2025Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆42Apr 27, 2026Updated 2 months 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.
- A package to draw custom heatmaps on molecular depictions of RDKit☆13Mar 31, 2022Updated 4 years ago
- Correlation-based feature selection of Molecular Dynamics simulations☆29Updated this week
- Adaptive sampling algorithms for molecular transitions☆29Jun 28, 2026Updated 3 weeks ago
- Water Network-Augmented Two-State model for Protein−Ligand Binding Affinity Prediction☆12Jun 10, 2023Updated 3 years ago
- C++ and Python library for Polarizable Embedding☆23Apr 27, 2026Updated 2 months ago
- Gromacs Topology Files for common Ionic Liquids☆24Jan 24, 2026Updated 6 months ago
- This program computes the sum-frequency generation (SFG) spectrum for a give MD trajectory of interfacial water molecules. The program ca…☆13Jul 24, 2023Updated 3 years ago
- ☆13Jun 10, 2024Updated 2 years ago
- RESP with inter- and intra-molecular constraints in Psi4.☆32May 26, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Enhanced sampling methods for molecular dynamics simulations☆45Dec 16, 2022Updated 3 years ago
- Trusted force field files for gromacs☆72Oct 31, 2024Updated last year
- Implementation of corrections for diffusion coefficients in membrane simulations.☆10Aug 2, 2022Updated 3 years ago
- 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
- Python implementation of the umbrella integration method for potential of mean force (PMF) calculations☆17Feb 4, 2019Updated 7 years ago
- Parameter/topology editor and molecular simulator☆451Jul 1, 2026Updated 3 weeks ago
- Code for designing biased protein states☆83Apr 15, 2026Updated 3 months ago