Index

Symbols

--angle-list command line option --axis command line option --bin-width command line option --box-type command line option --charged-CTD command line option --charged-NTD command line option --checkpoint command line option --cutoff command line option --cutoff-multiplier command line option --cutoff-scheme command line option --degree-extend command line option --delta-time command line option, [1], [2], [3], [4], [5], [6], [7] --dense-phase-threshold command line option --elastic-force-constant command line option --elastic-lower command line option --elastic-residues command line option --elastic-upper command line option --end-time command line option, [1], [2], [3], [4], [5], [6], [7] --forcefield command line option, [1], [2] --frame command line option --gap command line option --index command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9] --input command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9] --input-pdb command line option --input-structure command line option --input-topology command line option, [1] --mesh command line option --minimum-x command line option --minimum-y command line option --minimum-z command line option --modifications command line option --msd-type command line option --multiply-x-axis command line option --multiply-y-axis command line option --multiply-z-axis command line option --no-center command line option --number command line option, [1] --output command line option, [1], [2], [3], [4], [5], [6], [7], [8] --output-average command line option, [1] --output-conformation command line option, [1] --output-histogram command line option --output-inter-reference-reference command line option --output-inter-reference-selection command line option --output-inter-selection-selection command line option --output-intra-reference command line option --output-intra-selection command line option --output-name command line option --output-pair command line option --output-pair-statistic command line option --output-prefix command line option --output-residue command line option --output-residue-statistic command line option --output-structure command line option --output-time command line option, [1] --output-topology command line option, [1], [2], [3] --output-type command line option --output-verbose command line option, [1], [2], [3] --parameter command line option --pbc command line option --post-translational-modification command line option --radius command line option --reference command line option --reference-group command line option --residue-index command line option --run-input command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --selection command line option, [1], [2], [3], [4] --selection-calculate command line option, [1] --selection-fit command line option --selection-group command line option --sequence command line option --shuffle command line option --start-time command line option, [1], [2], [3], [4], [5], [6], [7] --structure command line option, [1], [2], [3] --time command line option

--time-step command line option --topology command line option, [1], [2] --trajectory command line option --treat-pbc command line option, [1], [2], [3], [4] --treat-pbc-x command line option --treat-pbc-y command line option --treat-pbc-z command line option --type command line option --x-axis command line option --y-axis command line option --z-axis command line option -al command line option -b command line option, [1], [2], [3], [4], [5], [6], [7] -bt command line option -bw command line option -c command line option -cCTD command line option -cm command line option -cNTD command line option -cpi command line option -cs command line option -dt command line option, [1], [2], [3], [4], [5], [6], [7] -e command line option, [1], [2], [3], [4], [5], [6], [7], [8] -ef command line option -el command line option -er command line option -eu command line option -f command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] -ff command line option, [1], [2] -fm command line option -g command line option -if command line option -ip command line option, [1] -m command line option, [1] -mesh command line option -mx command line option, [1] -my command line option, [1] -mz command line option, [1] -n command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -nc command line option -o command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9] -oa command line option, [1] -oc command line option, [1] -of command line option -oh command line option -on command line option -op command line option, [1], [2], [3], [4], [5] -ops command line option, [1] -or command line option, [1] -orr command line option -ors command line option, [1] -os command line option -oss command line option -ot command line option, [1], [2] -otype command line option -ov command line option, [1], [2], [3], [4] -p command line option, [1], [2] -pbc command line option, [1], [2], [3], [4], [5], [6] -ptm command line option -px command line option -py command line option -pz command line option -r command line option -ref command line option, [1] -ri command line option -s command line option, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] -sel command line option, [1], [2], [3], [4], [5], [6], [7] -selfit command line option -t command line option, [1], [2] -tp command line option -ts command line option -x command line option, [1] -y command line option -z command line option

A

anosotropy} command line option

atom command line option

C

charge} command line option command line option --angle-list --axis --bin-width --box-type --charged-CTD --charged-NTD --checkpoint --cutoff --cutoff-multiplier --cutoff-scheme --degree-extend --delta-time, [1], [2], [3], [4], [5], [6], [7] --dense-phase-threshold --elastic-force-constant --elastic-lower --elastic-residues --elastic-upper --end-time, [1], [2], [3], [4], [5], [6], [7] --forcefield, [1], [2] --frame --gap --index, [1], [2], [3], [4], [5], [6], [7], [8], [9] --input, [1], [2], [3], [4], [5], [6], [7], [8], [9] --input-pdb --input-structure --input-topology, [1] --mesh --minimum-x --minimum-y --minimum-z --modifications --msd-type --multiply-x-axis --multiply-y-axis --multiply-z-axis --no-center --number, [1] --output, [1], [2], [3], [4], [5], [6], [7], [8] --output-average, [1] --output-conformation, [1] --output-histogram --output-inter-reference-reference --output-inter-reference-selection --output-inter-selection-selection --output-intra-reference --output-intra-selection --output-name --output-pair --output-pair-statistic --output-prefix --output-residue --output-residue-statistic --output-structure --output-time, [1] --output-topology, [1], [2], [3] --output-type --output-verbose, [1], [2], [3] --parameter --pbc --post-translational-modification --radius --reference --reference-group --residue-index --run-input, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] --selection, [1], [2], [3], [4] --selection-calculate, [1] --selection-fit --selection-group --sequence --shuffle --start-time, [1], [2], [3], [4], [5], [6], [7] --structure, [1], [2], [3] --time --time-step --topology, [1], [2] --trajectory --treat-pbc, [1], [2], [3], [4] --treat-pbc-x --treat-pbc-y --treat-pbc-z --type --x-axis --y-axis --z-axis -al -b, [1], [2], [3], [4], [5], [6], [7] -bt -bw -c -cCTD -cm -cNTD -cpi -cs -dt, [1], [2], [3], [4], [5], [6], [7] -e, [1], [2], [3], [4], [5], [6], [7], [8] -ef -el -er -eu -f, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14], [15] -ff, [1], [2] -fm -g -if -ip, [1] -m, [1] -mesh -mx, [1] -my, [1] -mz, [1] -n, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11] -nc -o, [1], [2], [3], [4], [5], [6], [7], [8], [9] -oa, [1] -oc, [1] -of -oh -on -op, [1], [2], [3], [4], [5] -ops, [1] -or, [1] -orr -ors, [1] -os -oss -ot, [1], [2] -otype -ov, [1], [2], [3], [4] -p, [1], [2] -pbc, [1], [2], [3], [4], [5], [6] -ptm -px -py -pz -r -ref, [1] -ri -s, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13] -sel, [1], [2], [3], [4], [5], [6], [7] -selfit -t, [1], [2] -tp -ts -x, [1] -y -z anosotropy} atom charge} cubic Group, [1] mol} Optional, [1] x xy xz y yz z}

cubic command line option

G

Group command line option, [1]

M

mol} command line option

O

Optional command line option, [1]

X

x command line option xy command line option

xz command line option

Y

y command line option

yz command line option

Z

z} command line option