Coordinates (COORDS) Data Set Commands

 

Coordinate I/O tends to be the most time-consuming part of trajectory analysis. In addition, many types of analyses (for example two-dimensional RMSD and cluster analysis) require using coordinate frames multiple times. To simplify this, trajectory coordinates may be saved as a separate data set via the loadcrd command or createcrd action. Any action can then be performed on the COORDS data set with the crdaction command. The crdout command can be used to write coordinates to an output trajectory (similar to trajout).

Although COORDS data sets store everything internally with single-precision, they can still use a large amount of memory. Because of this there is a specialized type of COORDS data set called a TRAJ data set (trajectory), which functions exactly like a COORDS data set except all data is stored on disk. TRAJ data sets can be created with the loadtraj command. TRAJ data sets cannot be modified.

There are several analyses that can be performed using COORDS data sets, either as part of the normal analysis list or via the runanalysis command. Note that while these analyses can be run on specified COORDS data sets, if one is not specified a default COORDS data set will be created, made up of frames from trajin commands.

As an example of where this might be useful is in the calculation of atomic positional fluctuations. Previously this required two steps: one to generate an average structure, then a second to rms-fit to that average structure prior to calculating the fluctuations. This can now be done in one pass with the following input:

parm topology.parm7
loadcrd mdcrd.nc
# Generate average structure PDB, @CA only
crdaction mdcrd.nc average avg.pdb @CA
# Load average structure PDB as reference
parm avg.pdb
reference avg.pdb parm avg.pdb
# RMS-fit to average structure PDB
crdaction mdcrd.nc rms reference @CA
# Calculate atomic fluctuations for @CA only
crdaction mdcrd.nc atomicfluct out fluct.dat bfactor @CA

The following COORDS data set commands are available:

Command Description
combinecrd Combine two or more COORDS sets
crdaction Run a single Action on a COORDS set
crdout Write a COORDS set to a file
createcrd (Action) Create a COORDS set during a run
loadcrd Create or append to a COORDS set from a file
loadtraj Create special COORDS set where frames remain on disk
permutedihedrals Rotate specified dihedral(s) in given COORDS set by specific interval or to random values
reference Load a single trajectory frame as a reference
rotatedihedral Rotate specified dihedral to specified value or  by given increment