python 67 analysis 28 simulation 24 lammps 23 science 22 molecular-dynamics-simulation 21 machine-learning 21 computational-chemistry 19 molecular dynamics 17 molecular-simulation 16 chemistry 15 gromacs 15 simulations 10 trajectory-analysis 10 mdanalysis 10 data-analysis 9 molecular 9 materials-science 9 physics 8 clustering 8 interatomic-potentials 7 free-energy 7 Molecular Dynamics 7 MD 6 dft 6 dynamics 6 markov-model 6 bioinformatics 6 quantum-chemistry 6 pytorch 6 tensorflow 6 computational-biology 6 biophysics 6 computational-physics 6 molecular-mechanics 5 biochemistry 5 molecular-modeling 5 protein 5 enhanced-sampling 5 neural-network 5 monte-carlo 5 ase 5 python3 4 transport 4 tica 4 vasp 4 jax 4 namd 4 protein-structure 4 force-fields 4 dimensionality-reduction 4 openmm 4 modeling 4 hmm 4 visualization 4 LAMMPS 4 scientific-computing 4 deep-learning 4 diffusion 3 coarse-grained-molecular-dynamics 3 Gromacs 3 drug-design 3 data-science 3 amber 3 feature-extraction 3 msmbuilder 3 pca 3 pyiron 3 open-source 3 c 3 pdb 3 molecular-simulations 3 structural-biology 3 materials 3 md 3 free-energy-calculations 3 hdf5 3 atomistic-simulations 3 lammps-data 3 high-performance-computing 3 material-science 3 density-functional-theory 3 materials-informatics 3 soft matter 2 lammps-python-interface 2 rdkit 2 force-field 2 slurm 2 collective-variables 2 MDAnalysis 2 ion-channel 2 graph-neural-networks 2 psi4 2 ab-initio 2 parallel-computing 2 SMILES 2 particle 2 HPC 2 phonopy 2 theoretical-chemistry 2