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IITG Chemical engineering alumni

Many
OthersList of whos who of CL-IITG

PSF from any pdb file

Abhigyan
Molecular SimulationUsing vmd to create psf file for any pdb file

March 2018

The protein structure file (PSF) is an essential part of running any molecular simulation in the famous NAMD software. While the pdb files are available easily on various sites and resources, generating the psf file can be a nightmare. In this section, we use vmd to generate the psf file.

GRE Word list

Abhigyan
GradList of all the words important for GRE

Feb 2018

It's always hard to choose whether to mug up magoosh, barron, or kaplan. Switching from book to app to website can be daunting and at times a frustrating task. Here I club all the words together. You can see the meaning by hovering over a word and click on it to know more about the word. Ciao.

Molecular Simulation through the years

Abhigyan
Molecular SimulationA time lapse of Computational Simulations

Dec 2016

In the early nineteenth century, Boltzmann and Maxwell addressed the proposition of studying the movement of a large number of independent atoms. They, along with Gibbs, created Statistical Mechanics to replace the computation of averages over trajectory with computation of distribution function and calculating statistical average instead.
However, the turf of molecular simulation was awaiting its most important player, yet to enter the field, 'Computers'.

On time correlation functions

Abhigyan
Molecular SimulationA brief discussion on how to calculate the time cross-correlation.

Dec 2016

Correlation functions are an important part of molecular dynamics simualtions as the Green Kubo methods are based on it. These help in obtaining the transport properties such as, Viscosity, shear stress, etc. However, the calculation can be a bit daunting without some basic knowledge. Here, I will enlighten on the concept behind these functions, how to evaluate them , and also, how to average over the n time origins. Stay tuned.

Supercomputer Account (Param Ishan)

Abhigyan
OthersGetting an account in the supercomputer at IITG