Skip to content

Ion solvation free energy with spherical boundary conditions

License

Notifications You must be signed in to change notification settings

jeff231li/ion_solvation_openmm

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

19 Commits
 
 
 
 
 
 
 
 

Repository files navigation

Info

  • OpenMM python scripts to calculate solvation free energies of ions and charged molecules using spherical boundary conditions (SBC)
  • The ion/molecule is alchemically decoupled using the alchemy package as part of openmmtools and the free energy is estimated with MBAR.
  • The self-energy for molecules is calculated using a generalized Born equation derived in the paper below. The python script uses MDAnalysis to read in the trajectory file.
  • Right now the script reads in CHARMM psf and pdb files but the code can easily be modified to read in other structure files.

Setiadi, J. and Kuyucak, S., 2019. A simple, parameter-free method for computing solvation free energies of ions. The Journal of Chemical Physics, 150(6), p.065101.

About

Ion solvation free energy with spherical boundary conditions

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages