Published in CodeX·Jun 5Fixing Intel compiler’s unfair CPU dispatcher (Part 2/2)Testing the effect of patch on performance — In the previous part of this post, I mentioned a way of patching the binary files compiled with Intel compilers or linked to Intel MKL to circumvent the unfair CPU dispatcher. The patching should allow the usage of SIMD instructions and other optimizations for AMD processors as well. In this…Computer Science6 min read
Published in CodeX·Jun 5Fixing Intel compiler’s unfair CPU dispatcher (Part 1/2)A simple patch that improves performance on AMD processors — If you are someone who writes code in C, C++ or Fortran, chances are, you have heard about Intel C/C++ compiler and Intel Fortran compilers. In fact, in scientific computing, Intel compilers are often preferred instead of GNU or LLVM compilers because they provide a significant boost when it comes…Programming18 min read
Published in CodeX·Jul 28, 2021Running open-source software on Windows7 tips for porting a Linux-targeted source code to Windows — I am a chemistry student, but my first foray into programming was when I decided to go into computational chemistry. I had been using my old Windows laptop for as far back as I can remember. …Programming11 min read
Published in CodeX·Jul 19, 2021Compiling and running GROMACS natively on WindowsI have been working for a few months on a project on molecular dynamics (MD) simulations. I was not particularly familiar with MD simulations before this, but I had to learn to use NAMD and GROMACS — two very popular softwares that can run various type of calculations using force-fields…Chemistry13 min read
Jun 17, 2021Introduction to Molecular Modelling: Part 9 (Partial Charges)I’m back with another part of the series of blog posts that I started last year! This is part 9, here I will cover the calculation of partial charges. …Computational Chemistry7 min read
Nov 30, 2020Introduction to Molecular Modelling: Part 8 (Infrared Spectra)This is yet another part in my series of blogs about molecular modelling. This blog is going to be about predicting infrared spectrum of a molecule by calculation. Infrared (IR) spectrscopy is a routine procedure in undergrad organic labs, which helps mainly to detect the functional groups in a compound…Computational Chemistry5 min read
Nov 24, 2020Introduction to Molecular Modelling: Part 7 (Basis Sets in GAMESS)This is another part of my blog series on molecular modelling. I use GAMESS for the QM calculations, and Avogadro and wxMacMolPlt as the GUI. This post is going to be about basis sets, mainly about their usage in GAMESS, with a little bit of theory at the beginning. …Computational Chemistry10 min read
Published in The Startup·Nov 20, 2020Introduction to Molecular Modelling: Part 6 (Calculating Free Energy of Activation)This is another part of the series of blogs about molecular modelling, mainly about the actual usage of the software, rather than the detailed theory. The QM calculations are done with GAMESS, and visualisation with wxMacMolPlt. One of the main uses of quantum chemistry is to calculate the Gibbs free…Computational Chemistry8 min read
Nov 16, 2020Introduction to Molecular Modelling: Part 5 (Intrinsic Reaction Coordinate)This is a part of the series of blogs on the basics of molecular modelling. The QM program GAMESS is used for the calculations. This post follows part 4, where the optimization of a transition state(TS) is described. …7 min read
Nov 12, 2020Introduction to Molecular Modelling: Part 4 (Transition States)This is part of the ongoing series of blogs where I write about the how-to of the molecular modelling. This is mainly focused on the software side of it (GAMESS). Modelling transition states(TS) is important in studying chemistry. Not only can it give data about the Gibbs free energy of…Computational Chemistry7 min read
