OPC Water in GROMACS: Fixing the MW Virtual Site Topology

Overview The OPC (Optimal Point Charge) water model is one of the most accurate available for bulk water properties — reproducing density, self-diffusion coefficient, and dielectric constant to wi...

Jul 3, 2026 Computational Chemistry, Molecular Dynamics

Fixing Rigid Pd Cluster Topologies in GROMACS: Replacing Constraints with Stiff Bonds

Overview If you are running rigid metal nanoclusters in GROMACS and hitting either a “Cannot do constraint virial” fatal error or silent trajectory corruption where the cluster slowly deforms or e...

Jul 3, 2026 Computational Chemistry, Molecular Dynamics

Setting Up a Pd₄ Nanocluster in OPC Water for GROMACS MD Simulation

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...

Jun 20, 2026 Computational Chemistry, Molecular Dynamics

Setting Up a Pd₃ Nanocluster in OPC Water for GROMACS MD Simulation

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...

Jun 20, 2026 Computational Chemistry, Molecular Dynamics

Setting Up Pd Nanocluster MD Simulations: What Actually Worked

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...

Jun 20, 2026 computational-chemistry, molecular-dynamics

Two Pd₃ Nanoclusters in OPC Water — Diagonal Placement and GROMACS Setup

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...

Jun 20, 2026 Computational Chemistry, Molecular Dynamics

GROMACS Equilibration and Production Protocol for Solvated Nanoclusters

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)...

Jun 18, 2026 Computational Chemistry, Molecular Dynamics

Building pd4.ff — A Force Field File for the Pd₄ Cluster in fftool

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...

Jun 17, 2026 Molecular Dynamics, Force Field

Building pd3.ff — A Force Field File for the Pd₃ Cluster in fftool

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...

Jun 17, 2026 Molecular Dynamics, Force Field

Running a Pd3 Cluster in OPC Water: A Complete LAMMPS Simulation Guide

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...

Jun 17, 2026 Molecular Dynamics, HPC, Palladium, Solvation

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