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Ab-initio calculation of compound-water dimers

:::bash
~/$DIR/src/gas.phase.opt.sh mol.top mol.pdb mol.par atom_type_sel [Ncor]

Input arguments:

:::bash
mol.top: CHARMM-compatible topology file of the compound
mol.pdb: PDB file that contains a single conformation of the compound
mol.par: CHARMM-compatible parameter file
atom_type_sel: Set of atom types that will be most sampled
Ncor: number of cores used for the NAMD simulation

The first three arguments allow to generate the compound itself in NAMD. The compound is solvated in a box of TIP3P water (using generated VMD scripts), and run in NAMD using the approximate LJ parameters given by mol.par. At the end of the simulation, the trajectory is split in a number (1'000, currently) snapshots, where each snapshot only includes the compound and a water molecule that is close to one of the atom types in atom_type_sel.

All snapshots are then converted to Gaussian input files. The script then connects to a remote cluster (see config file) and submits all jobs to the queuing system. Once the jobs are finished, all output files are copied back to the local machine.