Slides

Sander: 1. Restrained Minimization
• Classical restrained minimiza4on of the system
– acetone is restrained to its ini4al posi4on
– water molecules are allowed to reorient, i.e. to solvate the
solute properly (e.g. forming hydrogen bonds, ...)
mpirun -np 8 sander.MPI ... &
-O overwrite output files if they exist
-i control data for Min/MD run: 1-restraint.inp
-o output file: eq_restraint.out
-c initial coordinates: acetone_solv.rst
(opt. velocities, periodic box size (last line))
-p topology file: acetone_solv.top
-r final coordinates, etc. (for restart):eq_restraint.rst
-ref reference coordinates for position restraints:
acetone_solv.rst
-inf latest mdout-format energy info: eq_restraint.info