Molecular Models

4.1 ms2

ms2 is a MD and MC code, mainly used for the computation of a large variety of thermodynamic bulk properties for pure substances and mixtures. The input file of the simulation program ms2 consists of a single file with the extension .pm. Each pm file contains the complete information about the force field of a molecular model and is independent form other pm file and the file specifying the simulation parameters. The pm files can be used directly without further modifications by the user. The force field of a molecular model can be specified in ms2 by the following interaction sites:

The brackets indicate the corresponding string expected by ms2. The force field in a pm file is defined by a sequence of keywords, to which a single value is assigned by means of a "=" sign. These keywords can be divided into keywords that describe the structure of the force field (e.g. the number of types of interaction sites used, etc.), or keywords that describe the specification of the individual interaction sites. The keywords are specified line by line -- certain rules regarding the sequence of keywords need to be hold. A comment line that will be ignored by ms2 can be inserted to pm files by starting a line with a hash symbol "#". The individual keywords and the order in which they are to be defined is specified in the following:

Each input file starts in the first line with the keyword "NSiteTypes", which indicates how many different types ("LJ126", "Charge", "Dipole", "Quadrupole") of interaction sites are used in the force field. After the specification of "NSiteTypes" in the pm file, the individual types of interaction sites are defined in separate and consecutive parts, each part starting with the keywords "SiteType" and "NSite". These keywords specify the type and number of interaction sites defined in that particular section, respectively. If a certain type of interaction site is not in fore field model, this corresponding section is not defined in the input file.

The different types of interaction sites are defined in the order: Lenard-Jones 12-6, point charge, point dipole, point quadrupole. The keywords "SiteType" and "NSite" are specified as:

SiteType = LJ126 NSites = X

where X stands for example for the number of Lennard-Jones 12-6 interaction sites used in the force field. Than, each individual interaction sites of the type "LJ126" is defined. Note that additional information that is not captured by the keywords, can be specified by the user by means of a comment using the hash symbol "#". The definition of a "LJ126" site has the folowing form:

# Name of the modeled atom(s) of the force field x = X y = X z = X sigma = Y epsilon = Y mass = Y

where X stands for the Cartesian coordinates and Y for the numeric value for the size, energy and mass parameter of the LJ126 interaction site, respectively. The corresponding units can be found in Table 1. The individual interaction sites have to be separated by at least one blank line. For each interaction site, the first thing to be specified is the name of the site by means of a comment. The naming of the individual LJ126 sites in this database is based on the part of the original molecule or atom that is modeled by the respective LJ126 site. In the following three lines, the position is defined by a global Cartesian coordinate system whose origin and orientation can be set as desired. This coordinate system is then used to define the positions of all subsequent interaction sites. In the next lines the type-specific parameters are defined, in this case the parameters for a Lennard-Jones interaction site are to be defined.

Only if the force field consists of point charges, the section for point charges occurs in a pm file. The definition of point charges is analogous to the definition of the Lennard-Jones 12-6 interaction sites. The definition of a single point charge consists of the following keyword sequence:

# e(i) x = y = z = charge = mass = shielding =

Analogous to the definition of the "LJ126" sites, a point charge is named first and than the position is defined in the already introduced global Cartesian coordinate system. pm files provided by the database have charges named by "e(i)", with $i \leq$ value of the keyword "NSites" that belongs to a section of point charges. An exception to this procedure are point charges which explicitly model a hydrogen atom -- are additionally indicated by "H[e(i)]".

In the following three lines, the type-specific parameters: magnitude of the charge "charge", mass "mass" and shielding "shielding" are defined. The units of the individual keywords can be found in section 4.1
.

If point dipoles or point quadrupoles are also used to define the force field, then the two sections are introduced accordingly and the individual sites are defined in sections as for the "LJ126" and "Charge" interaction sites. The definition of the individual sites then has the following form:

SiteType = Dipole NSites = X # d(i) x = y = z = theta = phi = dipole = mass = shielding = [...] SiteType = Quadrupole NSites = X # q(i) x = y = z = theta = phi = quadrupole = mass = shielding = [...]

The naming is analogous to that of the point charges. Without exception, the dipoles and quadrupoles are numbered consecutively with the terms "d(i)" and "q(i)", respectively. Subsequently, the position of an interaction site is defined in the global Cartesian coordinate system. Next, the definition of the orientation of the multipoles takes place by means of two angles $\theta$ "theta" and $\phi$ "phi", where $\theta$ is the inclination angle with respect to the $z$ axis and $\phi$ is the azimuthal angle with respect to the $x$−$z$ plane. Then the further type-specific parameters of the multipole are defined as the magnitude of the multipole "dipole" or correspondingly "quadrupole", the mass "mass" and the shielding "shieldinging". After defining the interaction sites, the "NRotAxes" variable is set to "auto".

As a full example of a ms2 pm file is given from the 'C2H4 I'-model published by Vrabec et al. [Vrabec, 2001] :

NSiteTypes = 2 SiteType = LJ126 NSites = 2 #CH2 (1) x = 0.0 y = 0.0 z = -0.63475 sigma = 3.7607 epsilon = 76.950 mass = 14.027 #CH2 (2) x = 0.0 y = 0.0 z = 0.63475 sigma = 3.7607 epsilon = 76.950 mass = 14.027 SiteType = Quadrupole NSites = 1 #q x = 0.0 y = 0.0 z = 0.0 theta = 0.0 phi = 0.0 quadrupole = 4.3310 mass = 0.0 shielding = 0.75214 NRotAxes = auto

pm input file for ms2 require the extension ".pm" and are encoded in ASCII/UTF-8. Tabs should be avoided and the numeric values should be formated either as regular floating point numbers (0.75214) or in exponential format (7.5214E2).