Usage

Taurenmd provides a command-line interface to many routines in Molecular Dynamics data analysis, therefore taurenmd runs by executing one-line and argument-rich commands on the terminal.

Taurenmd uses other scientific libraries to handle and generate Molecular Dynamics data. You SHOULD by all means cite also the other libraries when using taurenmd. Please refer to our Citing section for more detailed instructions.

We have several command interfaces already implemented, our Command-line interfaces page documents in detail each and every of them.

IMPORTANT

Do not forget to activate the python environment where you installed taurenmd in case it is not yet activated. Please read through our Installation page.

taurenmd main client interface.

Usage Examples

To access to the complete list of taurenmd commands with a summary information for each, execute:

>>> taurenmd -h

or simply:

>>> taurenmd

To see the current version number:

>>> taurenmd -v

Using trajedit as an example, lets inspect its functionality:

>>> taurenmd trajedit -h

With trajedit you can edit a trajectory in many different ways. For example, convert a trajectory to another format:

>>> taurenmd trajedit topology.pdb trajectory.xtc -d new_trajectory.dcd

The above command reads the original trajectory.xtc file and outputs the new new_trajectory.dcd. You can also use trajedit to reduce the trajectory size, say by slicing every 10 frames:

>>> taurenmd trajedit topology.pdb trajetory.xtc -d traj_p10.xtc -p 10

the -p option refers to the slicing step size, in this case 10 - reads every 10 frames. Likewise, you can pass a start (-s) and an end (-e) arguments:

>>> taurenmd trajedit topology.pdb trajectory.xtc -d traj_s50_e500_p10.xtc -s 50 -e 500 -p 10

Also, you can extract an Atom Selection from a trajectory to a new trajectory file. The example bellow creates a new trajectory from the input one containing only atoms belonging to chain A. In cases like this it is useful to extract the atom selection as an independent topology file.

>>> taurenmd trajedit top.pdb traj.xtc -l 'segid A' -d chainA.xtc -o chainA_topology.pdb

You can also use trajedit to extract a specific frame from a trajectory:

>>> taurenmd trajedit topology.pdb trajectory.xtc -d frame40.pdb -s 40 -e 41

but, for this example, you could instead use the fext interface:

>>> taurenmd fext topology.pdb trajectory.xtc -f 40 -x .pdb -f frame_

Each an every taurenmd sub command is available directly as a main routine by prefixing a tmd to its name, for example:

>>> taurenmd trajedit
>>> # equals to
>>> tmdtrajedit

Logging

taurenmd logs all its running activity as follows:

1. .taurenmd.cmd, keeps an historic register of the taurenmd commands run on a given folder together with a list of the research projects that must be cited for that particular run; these are the libraries taurenmd used to access and process the MD data. It also servers as a record for your research project.

2. .taurenmd.log, a user readable logging information, the very same that is printed in the terminal during runtime. Overwrites previous runs.

3. .taurenmd.debug, a full verbose log with all runtime information for the LAST run. Overwrites previous runs.