msi2lmp - Man Page

msi2lmp [-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]

MSI2LMP is a tool bundled with LAMMPS to aide in the conversion of simulation inputs from Biovia's Materials Studio software for use with LAMMPS. It is a standalone program that generates a LAMMPS data file based on the information in an MS .car file (atom coordinates), an .mdf file (molecular topology and atom types) and an .frc (forcefield parameters) file.  The .car and .mdf files are specific to a molecular system while the .frc file is specific to a forcefield (variant).  The only coherency needed between .frc and .car/.mdf files are the atom types.

-h,  -help,

Print detailed help message to the screen and stop.

<ROOTNAME>

This has to be the first argument and is a mandatory argument. It defines the root of the file names; i.e. for a <ROOTNAME> of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf' in the current working directory. msi2lmp will then read and process those files according to its remaining settings. All other settings are optional and have defaults as listed.

-c <I,1,II,2,O,0>, -class <I,1,II,2,O,0>

The -c or -class option selects the force field class, i.e which pair styles and bond styles and so on are required in the LAMMPS input file. Class I or class 1 uses similar combination of functional forms as Amber and Charmm force field and support the force fields cvff and clayff. Class II or class 2 corresponds to the more complex force fields COMPASS and pcff. Class O or class 0 finally is an experimental and incomplete extension and supports generating output for OPLS-AA

-f <ffname>, -frc <ffname>

The -c or -frc option allows the selection of the force field parameter file Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug, pcff, compass_published, cff91, and oplsaa. If the argument is a pathname, i.e. it starts with a '.' or a '/', then this absolute path is used to read the force field, otherwise msi2lmp will look in the folder pointed to by the environment variable $MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current directory. The extension '.frc' is appended, if missing. Default is to look for the cvff.frc force field file.

-p <loglevel>, -print <loglevel>,

Selects the amount of information messages about the progress of the conversion printed to the screen. <loglevel> can be a number from 0 (silent except for errors) to 3 (very detailed).

-i,  -ignore,

Ignore errors about missing parameters and use 0.0 for the respective force constants making these no-ops. Is correct to be used for a few molecules and settings, but often an indication, that either the atom type assignment have errors, or the force field file is missing entries.

-n,  -nocenter,

Do not center the box around the (geometrical) center of the atoms, but around the origin. Default is to recenter.

-o,  -oldstyle,

Write out a data file without style hint comments to be compatible with old LAMMPS versions. Default is to write out those comments.

-s <x> <y> <z>, -shift <x> <y> <z>,

Shift the entire system (box and coordinates) by a vector (default: 0.0 0.0 0.0).

msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc

msi2lmp benzene-class1 -c I

msi2lmp decane -c 0 -f oplsaa

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