SPICA-group / spica-toolsLinks
Tools for coarse-grained molecular dynamics simulations using the SPICA force field
☆12Updated 6 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:
- ☆28Updated last year
- Code to support the paper: P. van Gerwen, K. R. Briling, C. Bunne, V. R. Somnath, R. Laplaza, A. Krause, C. Corminboeuf, "3DReact: Geomet…☆23Updated 3 weeks ago
- ☆25Updated 3 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 10 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 4 months 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
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆40Updated last month
- A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4☆33Updated 4 months ago
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- Algorithm for identifying hydrogen bond networks in CG proteins to implement Go-like Martini 3 models☆13Updated 11 months ago
- Gromacs Implementation of OPLS-AAM Force field☆14Updated 7 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- ☆28Updated 5 months ago
- Q6 Repository -- EVB, FEP and LIE simulator.☆34Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- ☆30Updated 2 months ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆49Updated 4 years ago
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆18Updated 2 years ago
- Lee-Ping's general purpose script for running OpenMM molecular dynamics simulations☆30Updated last year
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆15Updated 3 years ago
- Conformer-Rotamer Ensemble Sampling Tool based on the xtb Semiempirical Extended Tight-Binding Program Package☆35Updated 2 months ago
- Robust Equilibration Detection☆25Updated last month
- Set up relative free energy calculations using a common scaffold☆24Updated 2 months ago
- Free Parametrization for Small Molecules☆45Updated last week
- ☆25Updated last year
- ☆39Updated last year