Setting Up Pd Nanocluster MD Simulations: What Actually Worked This post documents the complete, working setup for molecular dynamics simulations of palladium nanoclusters (Pd3 and Pd4) solvated i...

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...

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)...

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 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 “...