Overview This post documents the setup of a molecular dynamics simulation containing two Pd₃ palladium nanoclusters solvated in OPC water, where the clusters are placed 45 Å apart along the 3D box...

Overview This post documents the generic equilibration and production protocol used for all solvated nanocluster simulations in this series. The three-phase equilibration pipeline (EM → NVT → NPT)...

This post documents every decision made in constructing pd4.ff, the fftool-compatible force field file for a zero-valent palladium tetramer (Pd₄) cluster. It is a companion to the pd3-ff post and f...

This post documents every decision made in constructing pd3.ff, the fftool-compatible force field file for a zero-valent palladium trimer (Pd₃) cluster. Every number in the file is traced to a clea...

What this post covers: Every error, fix, and design decision encountered while setting up a production MD simulation of a Pd3 palladium nanocluster in OPC water — from force field files to HPC j...

GPU driver and CUDA Toolkit Install GPU driver using GUI GPU driver can be installed via other methods too but this is the easiest. Go to “Software & Updates”, go to “...

Using Supercomputer In this section you will learn how to submit or run your calculations on HPC (Supercomputer) using WinSCP Install WinSCP Go to official Website of WinSCP and install on your com...

Problem In this section we will try to simulate 500 atoms of carbon, in periodic(x,y,z) cubic box of dimentions 606060.Using LAMMPS code Disclaimer: Please dont rely on the accuracy of data...

IOT Project Instructions to connect Wemos_D1_mini(esp8266) When on the same Network Create a hotspot from your phone/desktop, rename your hotspot as “QMEL_LAB” and set the password of your ho...