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...

GROMACS Pipeline: Pd₃ in OPC Water Verified system state config.pdb — 21,618 ATOM records ✓ (3 Pd + 7205×3 OPC heavy/H sites) field.top — 2 × [ moleculetype ] ✓ (pd3 and OPC) run.mdp ...

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...

Overview This post documents the setup of a molecular dynamics simulation of a Pd₄ palladium nanocluster solvated in OPC water using GROMACS on the PARAM Shakti HPC cluster at IIT Kharagpur. It is...

Overview This post documents the complete pipeline for setting up a molecular dynamics simulation of a Pd₃ palladium nanocluster solvated in OPC water using GROMACS on the PARAM Shakti HPC cluster...

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...