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Notes on Molecular Dynamics simulation (MD)

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"The molecular dynamics problem is generally treated as a coupled set of differential equations. The system of differential equation  ...

Install and Use ASE (Atomic Simulation Environment) in Ubuntu Linux

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To install, I tried, pip install --upgrade --user ase /home/user/...../pip/_vendor/requests/__init__.py:83: RequestsDependencyWarning: ...

Running multiple jobs with qsub with uniqe names.

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I have a PBS script to run jobs. The name is specified by #PBS -N tag. But, if you want to run a number of files (100s, 1000s), it may be...

Removing permanent marker from Whiteboard

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Recently, I used permanent marker mistakenly instead of white-board marker. How to remove this writing? 1. If the writing is a few word...

Copy multiple files with different names (res to unres)

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Change directory to where you have the original files. Then test with the following command line, for i in *_original.*;do echo cp -p ...

Using for loop to save outcome in in different file using np.savetxt

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I wrote a script to do following task. For each number that is created using range(0,100), I created xyz coordinates to generate guess st...

awk, sed, pipe, grep, etc like functions in python

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I would like to translate from bash to python script. The bash contains awk, sed, pipes, cat commands. How to write commands in pyt...

Ubuntu update error: Unable to lock directory /var/lib/apt/lists/

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When I update using sudo apt-get update or sudo apt update I get following error. E: Could not get lock /var/lib/apt/lists/lock - o...

Trignometric formula

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Trig functions sin(A + B) = sin A cos B  +  cos A sin B cos(A + B) = cos A cos B  −  sin A sin B cos(A − B) = cos A cos B + sin A sin ...

Installing VESTA

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Check whether curl has been installed or not. which curl if curl is installed, it will give you the path.  If not installed,  ...