gromacs

Molecular dynamics simulation package for biomolecular research

brewmacoslinux

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Versatile package for molecular dynamics calculations

gmx

Preprocess a molecular dynamics simulation from structure and topology files$ gmx grompp -f md.mdp -c structure.gro -p topol.top -o md.tpr

Run a molecular dynamics simulation from prepared input$ gmx mdrun -deffnm md -v

Analyze trajectory and calculate root mean square deviation (RMSD)$ gmx rms -s md.tpr -f md.xtc -o rmsd.xvg