Post-Processing and Structural Analysis Pipeline for GROMACS MD Trajectories

Overview After a production run completes, two categories of analysis are required: Post-processing — thermodynamic validation (temperature, pressure, density, potential energy) confirming the...

Jul 3, 2026 Computational Chemistry, Analysis

COM-COM Distance Analysis with PBC Correction for Dual-Cluster MD Systems

The Problem: Naive Distance is Wrong Near Box Boundaries When two clusters are placed in a periodic simulation box, the apparent distance between their centres-of-mass can be misleading. Consider ...

Jul 3, 2026 Computational Chemistry, Analysis

Cluster-Size Distribution Analysis for Metal Nanoclusters Using MDAnalysis and SciPy

Overview Tracking cluster-size distributions over an MD trajectory answers a fundamental question in nanocluster chemistry: how does aggregation proceed over time? The measurement requires identif...

Jul 3, 2026 Computational Chemistry, Analysis

VMD Batch Snapshot Rendering for Publication Figures: The capture_frames.tcl Workflow

Overview Generating publication-quality snapshots from MD trajectories in VMD typically involves manually adjusting the view, setting representations, and clicking “Render” for each frame. For a p...

Jul 3, 2026 Computational Chemistry, Visualization

GROMACS 2026.2 with GPU Acceleration on Fedora 41: What Actually Works

System Specification OS: Fedora 41 (kernel 6.x) GPU: NVIDIA RTX 5000 Ada Generation (SM_8.9, 32 GB VRAM) CPU: Dual Intel Xeon Gold 6542Y (96 threads total, AVX-512) CUDA: 12.9 GROMACS: ...

Jul 3, 2026 Computational Chemistry, HPC Setup

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

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