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