SPICA-group / spica-toolsLinks
Tools for coarse-grained molecular dynamics simulations using the SPICA force field
☆11Updated 2 months ago
Alternatives and similar repositories for spica-tools
Users that are interested in spica-tools are comparing it to the libraries listed below
Sorting:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 6 years ago
- ☆27Updated last year
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆39Updated last week
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated 3 weeks ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆17Updated 2 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- ☆36Updated 9 months ago
- ☆29Updated last month
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Robust Equilibration Detection☆22Updated 2 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- TS2CG version 2☆13Updated last month
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆32Updated last week
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆14Updated last year
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Bayesian Multistate Bennett Acceptance Ratio Method☆13Updated last month
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- ☆28Updated last year
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 5 years ago
- RESP with inter- and intra-molecular constraints in Psi4.☆31Updated 2 years ago
- A tutorials suite for BioSimSpace.☆25Updated last month
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 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…☆23Updated last year
- Multiscale Simulation Tool for Backmapping☆17Updated 3 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆46Updated 4 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 6 months ago