Read Anim Molecule

Description

Read a molecule traiectory composed by molecular structures evolving along a set of time steps.

Input Ports

None

Parameters

file format list Select the format of the sequence to be read. The available formats are:
Kino
Format used by the prof. Parrinello group.
Multi PDB
Every step is in the same file. Each step starts with a HEADER line and ends with an END line.
DCD
The binary format produced by FMD. A traiectory is composed by two files: a pdb file and a dcd file. The DCD format is common to CHARMm, XPlor, and NAMD.
MultiFile PDB
Every step is a separate PDB file. The filename contains a sequential number.
Units list Measurement units used in the files. Currently the only format that uses Bohrs is the Gaussian Cube, not yet available for trayectories.
File name file browser The file name to be read or, for the MultiFile PDB format, the first file in the sequence.
DCD file name file browser The CDC file name to be read for the DCD format. This file browser appears only if DCD format has been selected.
Hydrogens toggle Enable Hydrogen atoms reading.
H bonds toggle Enable computation of H bonds.
Force Bonds Recomputation toggle Force bonds recomputation even if bonds definitions are already present in the file
Freeze bonds toggle Don't recompute bonds for every time step.
Bonding Range Adjustment slider Percentage of variation of the maximum distance between atoms to form a bond.
H Bonding Range Adjustment slider Percentage of variation of the maximum distance between H and an atom to form a bond.
H Bond Max Distance slider Maximum lenght of an H bond.
H Bond Max Angle slider Maximum angle HXY (in X__H..Y where .. is the H bond) to form an H bond.
Loop Loop module panel Cycle between the various steps. The first step is numbered 1 and the total number of steps is automatically computed from the input file.

Output Ports

molecule MolecularDataType Molecular data for each step.
step int Current step in the sequence. The steps are numbered starting from 1.

See also

An example of Kino format. First line: number of atoms, then a comment line, then atoms (symbol, x, y, z in Angstrom). Optionally another columnn is read as "charge" in the molecule output.

44
STEP: 0
AL  1.92648116963753 -3.28208460620044 -3.60914931585881
AL  0.46901642270632  1.20043438700265 -3.36518301597449
AL -0.41131779011742 -1.27093946611922  0.70223033040549
AL -2.00469211869004  3.34392169190793  0.62787176356185
AL -1.75618491401707  3.21296231482075  3.44552804599287
...
44
STEP: 1
AL  1.93413723593870 -3.27702099330197 -3.61617557823214
AL  0.45987711812727  1.20287643600264 -3.37015677594191
AL -0.40944987280746 -1.28086488373440  0.70110898401427
AL -2.00831506199881  3.33244408025349  0.61925422726264
AL -1.73425155583238  3.20873945312198  3.43392304489781
...