Descriptor File Format

boun: distance and angle constraint setting

The boun record defines sets of distance constraints which can be applied during molecular dynamics simulations. It is not necessary to have this record in order to run constrained molecular dynamics. It is possible to use the equilibrium bond lengths in the bond record to constrain bond distances for instance. The boun record has the form

boun
Nclass

1
Nbound

atomi
atomj
dij

...
...
...

...
...

where Nclass is the number of classes of constraints. Currently only one class, distance constraints, is available. Thus, Nclass must have the value 1. Following the header line is the data for the first class (distance constraints). The data starts with the class identifier which is the value 1, followed by the number of distance bounds Nbound, then Nbound lines containing three fields each. The fields are the atom pairs to be bounded atomi and atomj, and the distance to which they are to be bounded dij.


boun 1
1   5
1   2   34.0
2   3   34.0
3   4   34.0
4   5   34.0
5   1   34.0

Five atoms are laid single file on a closed curve (of indeterminate shape) and each atom is constrained to be 34Å from its two neighbors.


Details of Descriptor Records
intro
DES1
note
type
ivms
name
bond
mors
angl
angn
tors
itor
iton
nbn+
nbn-
ele+
ele-
vdw+
vdw-
abhb
noen
surf
stud
vlat
boun
lock

des format
arc format
yammp shell
exam commands
intro
arc
arcedit
arctransform
checkspider
des
elec2vlat

exam
mimesis
mkchainarc
mkchaindes
mkd3c
mkd3d
mkr2cc
mksnac
mksnad
xmd3
xmr2
ympf

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