-> Table of Contents
Moloc: Molecular Modelling on UNIX Workstations: 19 Dynamics [dyn]
Dynamics [dyn]
Various dynamics facilities are available here. Dynamics
can be run on all-atom and on Calf structures. Trajectory
files generated by batch runs (.mac or .mcc files) can be
viewed and analyzed.
In addition, graphs of energy versus one to three
torsional angles can be produced.
Furthermore, a few facilities provide interfaces to other
force field packages: GROMOS, XPLOR, and TNT.
,: peptide representation
h: drive dihedral angles
Up to three dihedral angles of a structure van be varied
systematically to produce one- to three-dimensional
energy maps.
d: dynamics of all atom structures
The MAB force field utility is entered with dynamics
being the default mode.
c: dynamics of Calf structures
The C-alfa force field utility (MCA) is entered with
dynamics being the default mode.
p,a: picked entry participates, active entries participate
If the trajectory deals with more than one entry,
option (a) is chosen here, and the appropriate starting
entries must be set active, while the remaining ones
must not. In the single-entry case this switch is set to
p (pick) and the menu items dealing with trajectory
evaluation are entered by picking the starting struc
ture.
b: set buffer size
By default the last 16 frames are kept in memory when a
trajectory is viewed. If more frames are needed this
can be changed here.
v: view trajectories
Reads and represents trajectory files generated by
batch dynamic runs. Depending on the type of structure
chosen, .mac or .mcc files are required. If the program
finds compressed versions (.Z) it reads those.
t: trajectory evaluations
Reads and analyzes trajectory files generated by batch
dynamic runs. Depending on the type of structure cho
sen, .mac or .mcc (.Z) files are required. Time graphs,
histograms and time correlation functions of various
quantities can be calculated.
e: examine files of time correlation functions
For large trajectory files the calculation of time cor
relation functions may be time consuming. In order to
keep such results available, they can be stored and
reexamined in this option.
m: show movie
A set of structures in memory can be sequentially dis
played to obtain an animated representation.
y: add explicit hyrogens for H-bonds
Taking all active entries, a hydrogen bonding pattern
is calculated. For every resulting H-bond the donor
hydrogen is explicitly added in an orientation that
optimally conforms with the position of the correspond
ing acceptor.
g: generate XPLOR (GROMOS) topology file
Topology and parameter files suited for the force
fields GROMOS and XPLOR and geometry files for the
refinement program TNT can be written here.
w: view GROMOS trajectory
The viewing utility is called (as under v) but the pro
gram expects a GROMOS trajectory file (.gmt).
Up to three torsional angles can be varied systematically
to produce an energy map. Previously produced maps can be
examined.
f: forge structure (see
Forge)
o: optimize structure (see
MAB-force field)
t: specify torsion
To specify a torsion, pick the corresponding bond. Then
a requester appears, asking for the initial value for
one of the possible torsion angles, the interval to be
scanned, and the number of steps in the interval. All
torsional angles possible with the specified bond will
be constrained at values corresponding to the ones ini
tially found (differences unchanged). Thus, it may be
advisable to start from a relaxed structure. To undo a
single specification pick the bond with the middle
mouse button.
r: reset specification
All previously specified dihedral angle data are dis
carded.
d: drive torsion
This choice leads to the actual performance of the cal
culation. One is first dropped into the menu for force
field settings, from where one can proceed in an inter
active or batch mode. For two- or three dimensional
problems, interactive mode is in most cases not advis
able.
m: select map
If a map file belonging to the current molecule has been
read and contoured in the map option, it may be selected
here for examination. If the atoms are uniquely
labelled and no specification of torsion angles is
already made (a reset may be advised), the appropriate
specification is automatically performed.
e: examine map
A selected map can be examined here as in the
map menu.
It is possible to adjust the current
conformation continuously to the value indicated by the
pointer position (see settings). When the energy value
is printed at the 3-d pointer position, in addition,
the corresponding angles are adjusted in any case to
the ones pointed at in the map.
p: 3d-pointer on <-> off
The 3-dimensional pointer is introduced at the position
corresponding to the current values of the specified
dihedrals.
s: settings
Two options can be set here: Presetting: Before the
optimization step the conformation can be set to the
one obtained from the initial conformation by giving
the specified dihedral angles the values they will be
constrained to during the following optimization. In
batch mode presetting is always done. Conformation
adjusting: When examining a map, the conformation of
the molecule can be continuously adjusted to the one
indicated by the position of the 3-d pointer.
Trajectories generated by dynamics batch-runs can be
viewed here. Various options to simplify the display
procedure are available.
g: geometry (see
Geometry)
i: initialize
If the trajectory is not in compressed form the viewing
process can be initialized by rewinding the file.
n: next configuration
With each click in this field the display advances to
the next frame.
a: advance by several frames
To advance in larger portions this field should be cho
sen.
m: movie
The frames are continuously read and displayed to yield
a movie of the trajectory.
p: foto movie
The frames are continuously read and displayed to yield
a movie of the trajectory. The display of the frames is
in the foto format.
f: foto
Show the display in foto format.
h: PostScript file
Makes a Encapsulated PostScript file (.eps) of the cur
rent view to be sent to a printer.
s: set step-size
Four parameters can be set here: 1. The number of steps
advanced with a n-click. 2. The number of frames
advances with an a-click. 3. the orientation mode (e.g.
automatic centering =1). 4. The number of frames over
which a running average is taken.
t: specify time per step in file
Recently produced trajectories should contain the
proper time scale. Here it can be reset. This concerns
mostly the actual time shown on the display.
c: comment for foto
A comment can be entered that will appear on the foto-
type displays.
k: keep structure
If a structure appears to be of interest it can be cop
ied to the set of existing structures in memory for
later use.
d,b: from disk
The origin of the frames can be from the disk file (d)
or from the memory buffer (b), if it is not empty. When
reading from buffer cycling takes place. The buffer
holds at most the number of frames specified in the
calling menu.
r,z: repositionable, centered
A mode can be set to have the picture repositionable (r)
interactively, or automatically centered (z).
e: examine energy
Calculates the energy of the current frame (may be
rather time-consuming) and enters the energy examina
tion menu.
v: average trajectory
An average structure over the trajectory is calculated.
,: peptide representation
Several quantities can be analyzed along a trajectory.
First the quantities of interest must be specified (e.g. a
distance) for which a analysis is required. In addition a set
of time values can be set that influence the mode of
evaluation. Upon choosing the type of analysis the user is
asked to specify a trajectory file. After evaluation of each
trajectory file the program asks for a continuation file. If
no such must be read, the file requester must be left with
the escape key. At this stage the program presents the
results as graphs. Correlation function and power spectrum
are displayed in two separate graphs.
l: list specifications
A list of specified values for which the trajectory
will be evaluated is presented.
i: specify time intervals
Several times are specifies: The time between frames
(More recent trajectories contain this information, but
it can be altered.); The number of steps per time unit
(as chosen for the spacing of consecutive points in the
correlation function); The number of time units to be
skipped at the beginning of the trajectory (equilibra
tion phase); and finally the number of time units the
correlation function should cover.
g: graph of trajectory
A graph of the specified quantities along the trajec
tory is produced. Averaging is done over as many steps
as indicated by the time unit in option i.
c: calculate correlation
Here the actual calculation of the time correlation
function is started, provided the specifications are
complete.
h: calculate histograms
Before the calculation of a histogram is started the
user must state the number of points (buckets) to be
used in the specified interval.
d: specify distances
Pairs of atoms can be specified. Their mutual distance
will be the quantity for which the calculations are
performed. The user is asked to specify upper and lower
limit. This is only of importance when histograms are
to be calculated, in order to specify the range over
which the histogram should extend.
t: specify torsion angles
Specify four consecutive atoms.
p: specify pyramidality
Specify a center and three ligands.
a: average data
Averages over a set of atoms are calculated. At present
the radius of gyration is implemented.
m: match rmsd to fixed structure
The root mean square deviation of a set of atoms of the
current structure from their position in a fixed one is
calculated after rigid body superposition. The set of
atoms is first specified. Then the user is asked for an
entry carrying the fixed conformation. The topology and
the arrangement of atoms of the entry is assumed to be
identical to the one of the running structure.
s: specify secondary structure content
Specify a segment of a Calf chain. For this segment the
helicity or (and) sheet content will be evaluated. The
wave-number of interest of the secondary structure, is
specified in option [0-6,g].
w: calculate power spectrum for secondary structure
The wave-number dependence of the specified secondary
structure is evaluated.
0-6,g: wave number, global
Wave-numbers from zero to six can be selected and a glo
bal value which corrects for boundary effects.
,: peptide representation
-> Table of Contents