TrajectoriesConcatenate workflow

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Description

 This workflow takes series of trajectories and concatenates them into one trajectory file named_TRAJ_CONCAT_VMD_(TIME_THE_FILE_IS_CREATED)

Required Software

 Kepler 2.4 or above
VMD 1.9.1 or above

Overview

 None

Usage

 There are two ways to run this workflow. One is through the graphic interface. After the workflowis opened, users can double-click the parameters to change their values and press the play button tostart. Another way is to run Kepler via a command line.

Parameters

pa Pattern. Default value is .*dcd$$ which will list all the .dcd files in theassigned directory.

d Directory. This should be a full path to the directory where all .dcd files are located.

p Topology file. This should be a full path of the toplogy file. For example, DIRECTORY/XXX.prmtop.

pt Topology type. Acceptable values are parm7 for Amber topology files and psf forCHARMM topology files. Default value is parm.

tt Trajectory type. Acceptable values are dcd for NAMD trajectories and pdb for PDBfiles. Default value is dcd.

ot Output trajectory type, indicates the desired type of output trajectories. Default value is dcd.

f First frame. This parameter tells VMD where to start extrapolating trajectories. It will applyto all the individual trajectory files. Default is 0 (starting from the first frame)

l Last frame. This parameter tells VMD where to stop extrapolating trajectories. It will applyto all the individual trajectory files. Default is -1 (ending at the last frame)

s Stride. This parameter tells VMD how many frames to be strided. For example, s = 2 means takeevery other frames, while s = 1 means to take all the frames. Default is 1.