namd
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Database of hand-built OPLS-AA parameters and topologies for 464 molecules. Zip files contains parameter and topologies for OpenMM, Gromacs, NAMD, CHARMM, LAMMPS, TINKER, CNS/X-PLOR, Q, DESMOND, BOSS and MCPRO.
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Aug 2, 2018
study of external electric fields' effects on the tubulin dimer via MD
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Dec 3, 2018 - Tcl
Longbow is a tool for automating simulations on a remote HPC machine. Longbow is designed to mimic the normal way an application is run locally but allows simulations to be sent to powerful machines.
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Jan 13, 2020 - Python
Tutorial for converting NAMD psf/pdb files to CHARMM PSF/CRD (credit attributed where appropriate to the AMAZING humans who developed these scripts)
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Sep 29, 2021
Perform molecular dynamics experiments (MD) with NAMD on colab
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Aug 20, 2022 - Jupyter Notebook
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
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Feb 6, 2023 - Tcl
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
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Feb 20, 2023 - Python
FabMD is a FabSim3 plugin for automated LAMMPS-based simulations.
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Mar 20, 2023 - Python
MDFF-EnTK: Scalable Adaptive Protein Ensemble Refinement Integrating Flexible Fitting
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Jun 8, 2023 - Slash
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
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Nov 14, 2023 - Python
All GROMACS/NAMD initializing files for generating initial structures for polydisperse chains with a set of residues desired by the user. With LigninBuilder, all lignin topologies can be built directly.
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Jan 15, 2024 - Python
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