pairwise

Calculate pair-wise non-bonded energies.

pairwise [<name>] [<mask>] [out <filename>] [cuteelec <ecut>] [cutevdw <vcut>] [ reference | ref <name> | refindex <#> ] [cutout <cut mol2 prefix>]
[vmapout <vdw map>] [emapout <elec map>] [avgout <avg file>] [eout <eout file>] [pdbout <pdb file>]

[<name>] Data set name; van der Waals energy will get aspect [EVDW] and electrostatic energy will get aspect [EELEC].
[<mask>] Atoms to calculate energy for.
[out <filename>] File to write total EELEC and EVDW to.
[eout <eout file>] File to write individual EELEC and EVDW interactions to.
[reference | ref <name> | refindex <#> ] Specify a reference to compare frames to (i.e. calculate Eref – Eframe).
[cuteelec <cut>] Only report interaction EELEC (or delta EELEC) if absolute value is greater than <ecut> (default 1.0 kcal/mol).
[cutevdw <cutv>] Only report interaction EVDW (or delta EVDW) if absolute value is greater than <vcut> (default 1.0 kcal/mol).
[cutout <cut mol2 prefix>] Write out mol2 containing only atom pairs which satisfy <ecut> and <vcut>.
[vmapout <vdw map>] Write out interaction EVDW (or delta EVDW) matrix to file <vdw map>.
[emapout <elec map>] Write out interaction EELEC (or delta EELEC) matrix to file <elec map>.
[avgout <avg file>] Print average interaction EVDW|EELEC (or average delta EVDW|EELC) to <avg file>.
[pdbout <pdb file>] Write PDB with EVDW|EELEC in occupancy|B-factor columns to <pdb file>.

Data Sets Created:
<name>[EELEC] Electrostatic energy in (kcal/mol).
<name>[EVDW] van der Waals energy in (kcal/mol).
<name>[VMAP] van der Waals energy matrix.
<name>[EMAP] Electrostatic energy matrix.

This action has two related functions: 1) Calculate pairwise (i.e. non-bonded) energy (in kcal/mol) for atoms in <mask>, or 2) Compare pairwise energy of frames to a reference frame. This calculation does use an exclusion list but is not periodic.

When comparing to a reference frame, the eout file will contain the differences for each individual interaction (i.e. Eref – Eframe), otherwise the eout file will contain the absolute value of each individual interaction. The cuteelc and cutevdw keywords can be used to restrict printing of individual interactions to those for which the absolute value is above a cutoff. The VMAP and EMAP matrix elements will contain these values as well (differences for reference, absolute value otherwise) averaged over all frames. The avgout file will contain only these values averaged over all frames that satisfy the cutoffs.

The cutout keyword can be used to write out MOL2 files each frame named ’<cut mol2 prefix>.evdw.mol2.X’ and ’<cut mol2 prefix>.eelec.mol2.X’ (where X is the frame number) containing only atoms with energies that satisfy the cutoffs. Similarly, the pdbout keyword can be used to write out a PDB file (with 1 MODEL per frame). The occupancy and B-factor columns will contain the total van der Waals and electrostatic energy for each atom ifcutoffs are satisfied, or 0.0 otherwise.