bioexcel / cp2K_qmmm_tutorials_for_biological_simulationsLinks
Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.
☆24Updated 6 years ago
Alternatives and similar repositories for cp2K_qmmm_tutorials_for_biological_simulations
Users that are interested in cp2K_qmmm_tutorials_for_biological_simulations are comparing it to the libraries listed below
Sorting:
- Temperature generator for Replica Exchange MD simulations☆30Updated 3 years ago
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆43Updated 2 months ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Updated last year
- ☆43Updated last year
- ☆31Updated last week
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated this week
- ☆24Updated 7 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆23Updated 11 years ago
- Adaptive string method implementation in AmberTools23 and Amber22☆14Updated last year
- Entropy from PDB conformational ensembles☆13Updated last year
- OpenMM scripts for polarisable molecular dynamics with the AMOEBA force field☆27Updated 5 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago
- easyPARM is a computational tool developed to simplify the derivation of force field parameters for metal-containing molecular systems an…☆32Updated last week
- PARENT: a parallel software suite for the calculation of configurational entropy in biomolecular systems☆16Updated 4 years ago
- A collections of scripts for working molecular dynamics simulations☆45Updated 6 months ago
- Set up relative free energy calculations using a common scaffold☆24Updated 5 months ago
- Free Parametrization for Small Molecules☆50Updated 3 months ago
- ☆13Updated 6 months ago
- Gromacs Implementation of OPLS-AAM Force field☆15Updated 7 years ago
- Useful Collective Variables for OpenMM☆17Updated last year
- A simple implementation of replica exchange MD simulations for OpenMM.☆24Updated 4 years ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆40Updated 2 years ago
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- ☆25Updated 2 years ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆11Updated 2 months ago
- Enhanced sampling methods for molecular dynamics simulations☆42Updated 3 years ago
- NAMD QM/MM Tutorial on Free Energy Profile of Reaction Mechanisms☆14Updated 7 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…☆24Updated last year
- Standalone charge assignment from Espaloma framework.☆46Updated 3 months ago