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DCD Reader from Toni Giorgino and Gianni De Fabritiis

Note: this patch is for MSMBuilder v 1.x only. The DCD reader is already included in the latest MSMBuilder releases.

People at http://www.multiscalelab.org made a DcdReader_patch to support DCD files in MSMBuilder. The patch extends the GromacsReader class into a DcdReader, which overrides the relevant IO methods. Reading of DCD trajectories is enabled by passing the -b/--dcdTrajectories flag to the doFastGromacsClustering and doFastGromacsAssign command lines. Note that, when using DCD files, units in the output will be Angstrom rather than nm.

The Python utilities have also preliminary support for DCD trajectories (also activated with the -b option). No topology/index files are required when using DCD trajectories (use /dev/null). Frame extraction is internally performed by calling the catdcd executable; coordinates are output is in the namdbin (.coor) format.

The modification is distributed as a patch file. DCD versions of the test XTC files are at dcd_files.tgz . Unit tests' outputs for XTC vs DCD are not binary-equal, but yield results within 10-5 A,which we believe to be due to the lossy compression in XTC files.

The patch applies to msmbuilder versions 1.0 and 1.0.1. To apply,

  1. download the msmbuilder source package and the patch file
  2. cd in the directory where you extracted msmbuilder

  3. issue the command   patch -p0 < DcdReader_patch 

  4. recompile

User Contributions (last edited 2016-05-04 22:06:54 by localhost)