fortan_dcd_analysis

Open/close, read, analyze dcd trajectories with python frontend and fortran backend

Requirements:

• Intel compiler
• Bash, linux environment
• Python 2
• catdcd https://www.ks.uiuc.edu/Development/MDTools/catdcd/

To use:

• Clone/copy the files into your location of choice/cluster

Conversion for .xtc to .dcd using catdcd

catdcd -o <dcdname> -xtc <xtcname> <optional>

To make a python usable module, run

Add the python2, intel, and gcc environment to the top of file "script"

./script "createmodule"

Example usage in python code in file : calculations.py

This file demonstates

• opening dcd file
• reading dcd header for #atoms, #frames information
• skips header when reading frames
• reading frames
• doing h-bond and first hydration shell calculation with distance and angle cutoff criteria

Test the python file on a N,P=1bar,T=300K simulation of SPC/E water in 5nm cubic box

To verify, you should see stuff printed on your terminal as contained in file "output"

Make sure you set the python2, intel, and gcc environment

./script "createmodule"

python calculations.py

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Quick and dirty use

module load python/2.7.15

module load gcc

module load intel

git clone https://github.com/ankur9511/fortan_dcd_analysis.git

cd fortan_dcd_analysis/

chmod +x ./script

./script "createmodule"

python calculations.py