MatDCD - Matlab package DCD reading/writing

Introduction

Features

  • supports Charmm and xplor-format DCD files
  • can read both big- and little-endian storage formats
  • can specify which atom indices to load; no need to load entire file

Limitations

  • Does not support dcd files with fixed atoms

Contact

If you have questions please send email to the author Justin Gullingsrud, at justin@ks.uiuc.edu

Download

License

Same terms as VMD license

Documentation

- matDCD: a DCD reader for Matlab -
Written by Justin Gullingsrud, based on the DCD code in VMD

* Features *
- supports Charmm and xplor-format DCD files
- can read both big- and little-endian storage formats
- can specify which atom indices to load; no need to load entire file

* Known issues *
- Does not support dcd files with fixed atoms

* Installation *
All the .m files in the distribution should reside in the same directory.
Place them anywhere you wish, then add that directory to your matlab path
using the matlab "addpath" command.

* Example usage *

1. alanin.dcd is a DCD file containing 100 frames of a 66 atom trajectory.
xyz will be a 100x198 matrix with each row containing coordinates in the
order [x1 y1 z1 x2 y2 z2 ...]

>> xyz = readdcd('/home/justin/alanin.dcd', 1:66);


2. Same dcd file; now we read only a list of selected atoms.

>>> atomlist = [2 5 9 13];
>>> xyz2 = readdcd('/home/justin/alanin.dcd', atomlist);

The rows of xyz2 will contain coordinates [x2 y2 z2 x5 y5 z5 ...]


3. Writing a DCD: say we modified xyz and want save it in a new DCD file.
We split the coordinates into separate arrays for the x, y, and z coordinates.
The syntax is:

x=xyz(:,1:3:end);
y=xyz(:,2:3:end);
z=xyz(:,3:3:end);
writedcd('alanin_new.dcd', x,y,z);