Parameters


The properties of all atom types as well as the parameters of all functional forms of the potential energy functions have to be supplied by the user. This can be done in a parameter file, which can have any name, as long as it is specified in the input file. The default name of the parameter file is parameters.ppf. In the parameter file 7 type of parameters can be set. These are

where the last one is a parameter that does not influence the simulation in any way, moreover it can be used be some visualization programs. For every type of parameter a specific format exists. These formats formats are discussed below. Specific values for parameters are always given in their corresponding SI-units. An example parameter file is included at the end of this section.

The parameter file ignores blank lines and lines starting with # as comments. In fact only lines starting with a ATOM, BOND, ANGL, TORS, IMPR, NONB or COLO keyword are processed. If more options than necessary for the format are supplied, they will be ignored.

Atoms

The atom properties to be set are the atom type, the mass and the Van der Waals radius. A line describing atom properties might look like: 

  ATOM H 56.1100 0.25254 0.0

The ATOM keyword indicates that we are dealing with atom properties, the second argument, in this case H, gives the atom type, the third argument is the mass (in amu) and the fourth argument is the Van der Waals radius (in nm). The last argument is only of importance when working with Langevin dynamics, since it is the damping frequency (per ps).

Bonds

A bonded pair of atoms is described by five parameters only, the two types of atoms making up the bond, the functional form of the interaction potential, the reference bond length and the force constant of the bond. In the PumMa parameter file, these parameters are expressed by a line such as: 

  BOND H O HARM 0.47295 3156.079

It is the first keyword BOND that indicates that we are dealing with bonded parameters. The two subsequent characters give the atom types for which these parameters are valid, in this example the bond is between H and O. Subsequently the functional form of the bond potential is given. Currently, the only accepted functional form is the harmonic potential, which is specified by the HARM keyword, see bonded potentials. Next the reference bond length (in nm) is given and finally the force constant belonging to the bond (in kJ/nm2). In the line above these are 0.47295 nm and 3156.079 kJ/nm2.

Angles

Depending on whether Urey-Bradley is compiled into the code (which is only useful when simulating fully atomistic models, not coarse grained models), seven or nine angle parameters are given in the parameter file. A line describing a non-Urey-Bradley angle, which is the most common to encounter, looks like: 

  ANGL H O C COSHARM 120.000000 5.40782

Again, the first keyword ANGL indicates the type of parameter that we are specifying, in this case angle parameters. The second, third and fourth characters specify the type of atoms these parameters are valid for, where the angle is between the first two and last two atoms respectively. In this example between HO and OC. As with the bond parameters, the functional form of the potential is given next. For angles this functional form can be either the harmonic potential (HARM) or the cosine harmonic potentials (COSHARM). The reference angle is given by the sixth argument (in degrees), whereas the last argument gives the force constant. The unit of the force constant depends on the functional form that is in use. In the case of a harmonic potential function the unit of the force constant is kJ/rad2, whereas when the cosine harmonic potential is used, the unit is kJ, since a cosine has no dimension. See the section on angle potentials for more details. In this example the reference angle is 120° and the force constant 5.40782 kJ, since the cosine harmonic form is used. When Urey-Bradley is used, the parameter line describing the angle is extended with two arguments, and looks like: 

  ANGL H O H COSHARM 120.000000 5.40782 1.12500 97.110

The eigth argument of this line (the first Urey-Bradley parameter) is the reference length of the Urey-Bradley interaction (in nm), whereas the nineth argument is force constant belonging to the Urey-Bradley interaction (in kJ/nm2). In this example they are 1.12500 nm and 97.110 kJ/nm2, respectively. Note that the Urey-Bradley potential is in fact a virtual bond between the first and third atom in the angle group, in this example between the two H.

Dihedrals

As with angles, dihedrals can be used in two functional forms in PumMa, a cosine and a harmonic form, see dihedral potentials for more details. For each of these forms the same parameter format can be used, however the force constant has a different unit in any of the two cases. The line that describes the dihedral parameters looks like: 

  TORS H O C N COS 100.000000 8.000000 1

The line starts again with a keyword indicating which parameter we are dealing with, in this case a dihedral specified by a TORS. The next four characters give the four atom types in the order of the normal definition of a dihedral, which means in consecutive order. In this case the order of the atoms is H, O, C and finally N. The dihedral angle then is the angle between the two planes HOC and OCN. Next the functional form of the dihedral potential is specified, which is either COS, for the cosine form, or HARM, for the harmonic form. The reference dihedral angle is the seventh argument to be specified (in degrees). Thereafter the force constant (depending on the functional form either in kJ/rad2 or kJ). The last argument is only valid for the case the cosine form is being used and gives the multiplicity, which is dimensionless, but always an integer variable. Although it is not needed by PumMa when the harmonic form is being used, the visualization converting program pumma2vmd expects an integer to be found at this position, hence it is a mandatory argument. This example has as reference angle 100°, as force constant 8 kJ/rad2 and as multiplicity 1.

For the cosine form the multiplicity defines the number of minima of the potential function. Hence, if a dihedral angle has three minima, the multiplicity (the last argument on the line) is three. If a dihedral angle has both local and global minima a combination of cosines can be used. In order to do so, each cosine of this combined function should appear on its own line. For example, a dihedral with two local minima at 90° and 270°, and a global minimum at 180°, has one line in the parameter file with multiplicity 3 (for the local minima and partly for the global minimum) and another line with multiplicity 1 (for the global minimum only). The combination of those two parameter lines, gives a combined cosine dihedral angle potential.

Impropers

An improper torsion is being used to maintain planarity around a certain atom. In PumMa a harmonic form of the improper torsion is assumed. Therefore, besides the four atom types that make up the improper torsion, only two other parameters need to be specified. The following line shows how improper torsions are specified in the PumMa parameter file: 

  IMPR N H H H HARM 60.000000 12.000000

As usual the first keyword specifies the type of parameter, in this case an IMPR for an improper torsion. The following four characters give the atom types which make up the improper torsion, where the first of the four is the central atom around which the planarity is maintained. The other three are the atoms surrounding this central atoms. For more details, see dihedral potentials. In this example the central atom is N, whereas the three surrounding atoms are all of the type H. Next the potential form is specified, which currently can only be the harmonic form (HARM). The seventh argument is the reference angle for the improper torsion (in degrees) and the final argument is the force constant belonging to the improper torsion potential (in kJ/rad2). For this specific example the reference angle is 60° and the force constant 12 kJ/rad2.

Van der Waals interactions

The only nonbonded parameter to be specified in the parameter file is for the Van der Waals interactions. For every interaction pair their parameters need to be given in the parameter file. For one such interaction the line might look like: 

  NONB H O LJ126 1.000000

The NONB indicates that this line gives the parameters belonging to a nonbonded interaction pair. The next two arguments give the atom types for this interaction pair, in this case between H and O. The fourth arguments indicates the potential we are dealing with. This can be either a 'true' Lennard-Jones potential (LJ126) or a truncated Lennard-Jones potential, which is a normal Lennard-Jones potential cut off in its minimum and shifted to be continuous (indicated by a TLJ126). Other possibilities are a Lennard-Jones 9-6 potential (LJ96), a Lennard-Jones 10-4 potential (LJ104), a Lennard-Jones 9-4 potential (LJ94) or a potential read from file (FILE). The last argument is the interaction strength belonging to this pair, the ε from the Lennard-Jones potential, and is expressed in units of kJ/mol. In this example the interaction strenghth is unity. When a potential is read from file this last argument is redundant. However, in the input options file the option NBtablefile has to be specified.

Colors

As mentioned before, colors are not important for the simulation, but they are useful in the graphical application in the PumMaTK program. A color line could look like: 

  COLO H 0.30 0.30 1.00

Of course, the first argument COLO indicates that a color is being specified, and the second argument specifies the atom type for which this color is valid, for this example H. The next three values are the RGB-values to specify the color. This specific set of values (0.30-0.30-1.00) gives a somewhat blueish atom.

Example file

In this example file the bond and angle harmonic potentials for the bonded interactions and the Lennard-Jones potential for the non-bonded interactions are used. 

  ATOM G 56.110000 0.252540
  ATOM T 56.110000 0.252540
  ATOM W 72.045240 0.258615
  BOND G G HARM 0.472950 3156.079012
  BOND G T HARM 0.472950 3156.079012
  BOND T T HARM 0.472950 3156.079012
  ANGL G G G HARM 180.000000 5.407820
  ANGL G G T HARM 180.000000 5.407820
  ANGL G T G HARM 180.000000 5.407820
  ANGL G T T HARM 180.000000 5.407820
  ANGL T G T HARM 180.000000 5.407820
  ANGL T T T HARM 180.000000 5.407820
  NONB G G LJ126 3.932960
  NONB G T TLJ126 1.966480
  NONB G W LJ126 3.932960
  NONB T T LJ126 1.966480
  NONB T W TLJ126 1.966480
  NONB W W LJ126 3.932960
  COLO G 1.00 1.00 1.00
  COLO T 0.50 0.90 0.40
  COLO W 0.30 0.30 1.00

This parameter file can also be downloaded from the download page.

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