Simulations with BOSS require a structure specified in Z-matrix. In case of molecular mechanics calculations, the Z-matrix defines OPLS-AA atom types and molecular connectivity. The Z-matrix file also contains information about bonds that are rotatable in flexible molecules. BOSS Z-matrixes can be conveniently created using the autozmat utility program. If you have obtained the structure of a desired molecule in the PDB format, you can type:
autozmat -i pdb -o boss -z default < molecule.pdb > molecule.z
The file molecule.z needs further editing because autozmat does not assign OPLS-AA atom types based on its perception of molecular structure. In other words, the user must define atom types in the third column. If alchemical mutations are performed as in FEP calculations, atom types for the mutated molecule shall be given in the fourth column. Recent versions of BOSS can figure out the necessary stretching, bending, and torsion parameters based on atom types but user can define these explicitly if necessary instead of AUTO assignments. To define additional bonded parameters explicitly, replace "default" keyword towt "varadd" keyword when running autozmat.
Simulation parameters such as temperature, solvent box size, extent of random moves, and many others are defined in the header files. It is common to use slightly different header files for NVT and NPT calculations. User should modify the parameters appropriately based on the requirements of the simulation. The content of the header file is described in the BOSS manual. The header files are combined with the nonbonded parameter file before the simulation starts into files called NVTpar and NPTpar
A complete simulation of a liquid typically consists of several simulation. It is a good idea to perform a brief NVT simulation such that molecules could alleviate any bad contacts which otherwise would lead to unwanted expansion. The following NPT simulation is typically divided into equilibration phase, during which the properties such as energy and volume of the system may change systematically, and an averaging phase, during which the properties of the system fluctuate randomly. The data during the averaging phase is used to characterize the system. The averaging is carried out in batches in order to minimize the use of computer memory and to check that the fluctuations in system properties are random: the results from batch to batch should not show systematic trends. The sequence of commands that executes such batches is collected into one command file. You need to change the number of batches, or the size of a batch when changing the number of simulation steps.
The /home/chem226/iproh_source directory contains iproh.z structure file. However, the parameter files are these for ethanol, and these lack some parameters needed for 2-propanol. Inspect files oplsaa.sb and oplsaa.par in $BOSSdir (more $BOSSdir/oplsaa.sb) and append missing parameters to the force field files. Edit the header files appropriately. Start with a box of 512 water molecules; the final number could be 508 because isopropanol will occupy the space of approximately 4 water molecules.
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