bident3 calculates contact types (e.g. monodentate, bidentate etc.) between defined sites on two species, as described for bident2, but in addition outputs distance histograms and distance-angle maps for each site and contact type.

Related Programs

  • To calculate contact distributions, see bident2.

Basic Usage

bident3 <HISTORYfile> <OUTPUTfile> <sp1> <sp2> <i> <j> <maxdist> [-frames n] [-discard n] [-site a b] [-dump] [-bin width]

Where:

  • <HISTORYfile> is the name of the DL_POLY HISTORY file
  • <OUTPUTfile> is the name of the DL_POLY OUTPUT file
  • <sp1> is the integer index of the species possessing the target 'H' atom sites
  • <sp2> is the integer index of the species possessing the 'bidentate' interaction sites
  • <i> is the integer index of the first atom of the bidentate binding site on species 2
  • <j> is the integer index of the second atom of the bidentate binding site on species 2
  • <maxdist> is the maximum allowable distance between sites on the two species

Although this is enough to run bident3, at least one 'H' site on species 1 must be defined with the -site option.

Switches

-bin width

Set the bin width used in distance histograms and the distance component of angle maps to width Angstroms (default = 0.05).

-discard n

Skip n frames at the beginning of the trajectory before starting the calculation (default = 0)

-dump

Print lots of individual contact information to a dump file.

-frames n

Stop calculating after processing n frames (default = all frames)

-site a b

Add a site a-b on species 1, where a and b are the local integer indices of the atoms. a represents the 'H'-type atom, and b its bound neighbour. Multiple sites may be defined at once, and will be considered separately in the output.

Output

Given an input HISTORY file results.HISu, then output files are as follows: results.bidentNNMM : all contact information for the defined sites between species NN and MM results.single_NNAABB_MMIIJJ.dist : distance histogram for single contacts between species NN atom AA and species MM atoms II and JJ results.bident_NNAABB_MMIIJJ.dist : distance histogram for bidentate contacts between species NN atom AA and species MM atoms II and JJ results.bridge_NNAABB_MMIIJJ.dist : distance histogram for bridging contacts between species NN atom AA and species MM atoms II and JJ results.bifur_NNAABB_MMIIJJ.dist : distance histogram for bifurcated contacts between species NN atom AA and species MM atoms II and JJ results.single_NNAABB_MMIIJJ.surf : distance-angle map for single contacts between species NN atom AA and species MM atoms II and JJ results.bident_NNAABB_MMIIJJ.surf : distance-angle map for bidentate contacts between species NN atom AA and species MM atoms II and JJ results.bridge_NNAABB_MMIIJJ.surf : distance-angle map for bridging contacts between species NN atom AA and species MM atoms II and JJ results.bifur_NNAABB_MMIIJJ.surf : distance-angle map for bifurcated contacts between species NN atom AA and species MM atoms II and JJ

All surf files are three-column format - distance, angle, histogram value - with distinct angles separated by blank lines.