20.5 Time Series Specifications

In this section, we describe what time series can be calculated for use by the correlation functions.

20.5.1 Syntax

                          { ATOM     atom-correl-spec              }
                          { BOND     bond-correl-spec              }
                          { ANGLE    angle-correl-spec             }
                          { TORSION  torsion-correl-spec           }
                          { IMPROPER improper-torsion-correl-spec  }
                          { VECTOR   vector-correl-spec            }
                          { SCP/VEC          vector-correl-spec    }
     correlation-spec ::= { CRS/SCP/VEC      vector-correl-spec    }
                          { SCP/ATM          atom-correl-spec      }
                          { CRS/SCP/ATM      vector-correl-spec    }
                          { FLCT/ATM         atom-correl-spec      }
                          { SCP/FLCT/ATM     atom-correl-spec      }
                          { CRS/SCP/FLCT/ATM vector-correl-spec    }
                          { RSQ/ATM          atom-correl-spec      }
                          { GYRATION         real                  }
                          { DENSITY          real                  }
                          { MODE                                   }
                          { TEMP                                   }

20.5.2 Function

The correlation-spec option is required. This option specifies the property for which the time dependence is sought. The program determines whether the correlation function requested is auto or cross correlation. When a colon appears in the middle of correlation-spec, the program assumes that a cross correlation has been requested between the quantities on either side of the colon. (In special cases like SCP/ATM, SCP/VEC, SCP/FLCT/ATM, which are auto correlation quantities, a colon may be needed .)

The options in correlation-spec are the same for both coordinates and velocities . Those options that are exclusive to coordinates (c) or velocities (v) are thus noted. The Time series is determined for one (auto) or two (cross) quantities desired. If more than one quantity is specified, then the average of those quantities are determined as the time series. For example,

     ATOM A 1 CA               ! auto correlation for first alpha carbon
     ATOM A 1 CA : A 2 CA      ! cross correlation between first and second
                               ! alpha carbons.
     ATOM A 1 CA : A 1 CB $ -
          A 2 CA : A 2 CB $    ! cross correlation between the average of
                               ! alpha carbons in residues 1 and 2 and the
                               ! average of beta carbons in residues 1 and 2.

The options are listed below with the property they represent.

ATOM atom-correl-spec

Positions of atoms or velocities.

BOND bond-correl-spec

Bond lengths (GEOMETRY) or energies (ENERGY).

ANGLE angle-correl-spec

Bond angles or bond angle energies.

TORSION torsion-correl-spec

Torsion angles or energies.

IMPROPER torsion-correl-spec

Improper torsion angles or energies.

VECTOR vector-correl-spec

Vectors joining pairs of atoms. (c)

SCP/VEC vector-correl-spec

Auto correlation for the scalar product of pairs of vectors. If the two vectors in each pair or not identical, the colon is used to distinguish the two vectors.

CRS/SCP/VEC vector-correl-spec

Cross correlation for the scalar product of two pairs of vectors. Note that even number of vectors are required on either side of the colon.

SCP/ATM atom-correl-spec

Auto correlation for the scalar product of the positions of atoms. If the atom pairs are not the same then a colon is used.

CRS/SCP/ATM vector-correl-spec

Cross correlation for the scalar product of the positions of atoms. Note that the atom pairs are described as vectors.

FLCT/ATM atom-correl-spec

Fluctuations of atom positions.

SCP/FLCT/ATM atom-correl-spec

Auto correlation for the scalar product of fluctuations of atoms. If the atom pairs are not the same then a colon is used.

CRS/SCP/FLCT/ATM vector-correl-spec

Cross correlation for the scalar product of the fluctuations of atoms. Note that the atom pairs are described as vectors.

RSQ/ATM atom-correl-spec

Square of the radial distance of the atom from the center. (c) Kinetic energy of the atom. (v)

GYRATION real

The radius of gyration of the molecule calculated using a cut-off given by the real number.

DENSITY real

The particle density of the molecule calculated using a cut-off given by the real number.

MODE

Projects the mass-weighted coordinates into the specified normal mode.

TEMP

The temperature of the molecule. (v)

The following are the syntax of the specifications used above.

     atom-correl-spec ::= repeat(atom-spec [: atom-spec] del)
     
     bond-correl-spec ::= repeat(atom-spec - atom-spec
                                 [: atom-spec - atom-spec] del)
     
     angle-correl-spec ::= repeat(atom-spec - atom-spec - atom-spec
                                  [: atom-spec - atom-spec - atom-spec ] del)
     
     torsion-correl-spec ::=
          repeat(atom-spec - atom-spec - atom-spec - atom-spec
                 [: atom-spec - atom-spec - atom-spec - atom-spec ] del)
     
     vector-correl-spec ::= repeat(atom-spec - atom-spec
                                  [: atom-spec - atom-spec] del)
     
     atom-spec ::= [segid] [resid] [iupac]

NOTE: The unnamed parts of an atom-spec default to those used previously in the individual correlation specification.