:::bash
~/$DIR/src/liquid.sims/charmm.sims.from.mc.sh file.top \
  file.par file.pdb file.lpun TEMP M file.dat maxEnergy [processID]

Input arguments

:::text
file.top: CHARMM-compatible topology file
file.par: CHARMM-compatible parameter file
file.pdb: PDB file of a single molecule
file.lpun: lpun file for MTP electrostatics (otherwise, provide "pc")
TEMP: temperature corresponding to the experimental data [K]
M: Molar mass of one molecule [g/mol]
file.dat: set of trial parameters from Monte Carlo simulation
maxEnergy: maximum energy of trial parameters (left-most column in file.dat)
processID: analyze previous run with process ID processID

Notes

1. file.dat is obtained from a Monte-Carlo parameter variation. Note that it's possible to filter such file to avoid sets that are too close
2. The script requires the initial configuration of a pure-liquid system

Output

The script will generate and submit CHARMM simulations with all selected (i.e., less then maxEnergy) sets of parameters to a remote cluster (see config file). After all gas and NPT simulations have completed, the script computes the density and heat of vaporization for each set.

In case a run has crashed, the existing data can be recovered by reading the processID of the previous run (the process ID can be read from the directories created for the trial simulations).

Once completed, the best parameters can be identified using experimental data, see Extracting sets close to experimental data for Monte-Carlo variation.