Blog

Blog & Research Articles

I write about molecular dynamics, chemical engineering, scientific computing, and research methodology.

Focus Areas:

Molecular dynamics simulation techniques and best practices
Force field development and validation
Data analysis and scientific computing with Python
HPC and performance optimization
Research tutorials and technical deep-dives
Scientific programming and open-source development

Recent Articles

### [Post-Processing and Structural Analysis Pipeline for GROMACS MD Trajectories](/posts/post-process-structural-analysis/) **Date**: July 03, 2026 **Categories**: Computational Chemistry Analysis **Tags**: #gromacs #python #mdanalysis #rdf #msd #diffusion #rmsd #post-processing #structural-analysis The complete post-processing and structural analysis pipeline for GROMACS MD trajectories — extracting thermodynamic properties, RDF, coordination number, MSD, diffusion coefficients, RMSD, and solvent shell analysis using gmx tools and Python, with the exact GROMACS 2026.2 syntax changes. [Read More →](/posts/post-process-structural-analysis/) --- ### [COM-COM Distance Analysis with PBC Correction for Dual-Cluster MD Systems](/posts/com-com-distance-pbc/) **Date**: July 03, 2026 **Categories**: Computational Chemistry Analysis **Tags**: #mdanalysis #pbc #com #cluster #aggregation #python #gromacs #distance Why naive inter-cluster distance calculations give wrong results near periodic box boundaries — and the exact MDAnalysis pipeline using minimize_vectors to compute PBC-correct centre-of-mass distances, moving averages, and aggregation timescales from GROMACS trajectories. [Read More →](/posts/com-com-distance-pbc/) --- ### [Cluster-Size Distribution Analysis for Metal Nanoclusters Using MDAnalysis and SciPy](/posts/cluster-size-distribution-mdanalysis/) **Date**: July 03, 2026 **Categories**: Computational Chemistry Analysis **Tags**: #mdanalysis #scipy #cluster #aggregation #python #palladium #connected-components A complete Python pipeline for tracking how metal nanocluster fragments evolve and coalesce over an MD trajectory — from distance matrix to connected components to fractional frequency histograms — using MDAnalysis and scipy.sparse.csgraph. [Read More →](/posts/cluster-size-distribution-mdanalysis/) --- ### [VMD Batch Snapshot Rendering for Publication Figures: The capture_frames.tcl Workflow](/posts/vmd-batch-rendering/) **Date**: July 03, 2026 **Categories**: Computational Chemistry Visualization **Tags**: #vmd #tcl #rendering #publication #molecular-dynamics #snapshots #batch A complete guide to automated VMD snapshot rendering for publication-quality figures — extracting exact view matrices from a live VMD session, drawing PBC boxes as graphics objects, and batch-processing 30+ trajectory systems without manual intervention. [Read More →](/posts/vmd-batch-rendering/) --- ### [GROMACS 2026.2 with GPU Acceleration on Fedora 41: What Actually Works](/posts/gromacs-gpu-fedora-setup/) **Date**: July 03, 2026 **Categories**: Computational Chemistry HPC Setup **Tags**: #gromacs #gpu #fedora #cuda #rtx5000 #avx512 #installation #performance Exact build flags, GPU offload options, and the specific combinations that fail silently on GROMACS 2026.2 with RTX 5000 Ada on Fedora 41 — so you do not have to rediscover them the hard way. [Read More →](/posts/gromacs-gpu-fedora-setup/) --- ### [OPC Water in GROMACS: Fixing the MW Virtual Site Topology](/posts/opc-water-gromacs-topology/) **Date**: July 03, 2026 **Categories**: Computational Chemistry Molecular Dynamics **Tags**: #gromacs #opc #water #topology #virtual-sites #settle #troubleshooting A complete guide to the non-obvious topology errors that occur when using OPC 4-site water in GROMACS — duplicate constraints blocks, missing MW virtual site entries, and SETTLE incompatibilities that silently corrupt your simulation or crash grompp. [Read More →](/posts/opc-water-gromacs-topology/) --- ### [Fixing Rigid Pd Cluster Topologies in GROMACS: Replacing Constraints with Stiff Bonds](/posts/pd-cluster-constraint-fix/) **Date**: July 03, 2026 **Categories**: Computational Chemistry Molecular Dynamics **Tags**: #gromacs #palladium #topology #constraints #force-field #troubleshooting How to fix the "closed constraint network" crash in GROMACS when simulating rigid Pd3 and Pd4 nanoclusters — replacing [ constraints ] with stiff [ bonds ] to survive GPU-offloaded MD without silent trajectory corruption. [Read More →](/posts/pd-cluster-constraint-fix/) --- ### [Setting Up a Pd₄ Nanocluster in OPC Water for GROMACS MD Simulation](/posts/pd4-h2o-gmx/) **Date**: June 20, 2026 **Categories**: Computational Chemistry Molecular Dynamics **Tags**: #gromacs #molecular-dynamics #palladium #opc-water #hpc #param-shakti #fftool #packmol #pd4 #tetrahedron A complete, reproducible pipeline for preparing and equilibrating a Pd₄ tetrahedral palladium nanocluster solvated in OPC water using GROMACS. Covers force-field preparation, 6-constraint rigid tetrahedron topology, 4-site OPC virtual-site correction, and the full EM → NVT → NPT protocol on PARAM Shakti HPC. [Read More →](/posts/pd4-h2o-gmx/) --- ### [Setting Up a Pd₃ Nanocluster in OPC Water for GROMACS MD Simulation](/posts/pd3-h2o-gmx/) **Date**: June 20, 2026 **Categories**: Computational Chemistry Molecular Dynamics **Tags**: #gromacs #molecular-dynamics #palladium #opc-water #hpc #param-shakti #fftool #packmol A complete, reproducible pipeline for preparing and equilibrating a Pd₃ palladium nanocluster solvated in OPC water using GROMACS on an HPC cluster. Covers force-field preparation with fftool/Packmol, 4-site OPC virtual-site topology, energy minimisation, NVT and NPT equilibration, and automated sanity checks. [Read More →](/posts/pd3-h2o-gmx/) --- ### [Setting Up Pd Nanocluster MD Simulations: What Actually Worked](/posts/pd-cluster/) **Date**: June 20, 2026 **Categories**: computational-chemistry molecular-dynamics **Tags**: #gromacs #palladium #opc-water #nmp #lincs #cuda #vmd 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 in OPC water, NMP, and mixed water/NMP environments. It covers the build pipeline, the topology corrections that were actually necessary, a serious constraint... [Read More →](/posts/pd-cluster/) --- ### [Two Pd₃ Nanoclusters in OPC Water — Diagonal Placement and GROMACS Setup](/posts/2pd3-h2o-gmx/) **Date**: June 20, 2026 **Categories**: Computational Chemistry Molecular Dynamics **Tags**: #gromacs #molecular-dynamics #palladium #opc-water #hpc #param-shakti #fftool #packmol #multi-cluster Setting up a GROMACS MD simulation of two Pd₃ nanoclusters separated by 45 Å along the 3D box diagonal in OPC water. Covers diagonal placement geometry, multi-cluster pack.inp, topology with count=2, MW insertion, and the full equilibration pipeline on PARAM Shakti HPC. [Read More →](/posts/2pd3-h2o-gmx/) --- ### [GROMACS Equilibration and Production Protocol for Solvated Nanoclusters](/posts/gromacs-equilibration-production/) **Date**: June 18, 2026 **Categories**: Computational Chemistry Molecular Dynamics **Tags**: #gromacs #molecular-dynamics #equilibration #production #npt #nvt #energy-minimisation #hpc #param-shakti #slurm A generic, reusable protocol for GROMACS energy minimisation, NVT and NPT equilibration, and NPT production runs on PARAM Shakti HPC. Covers MDP parameter rationale, SLURM submission, post-run sanity checks, PBC correction, and checkpoint-based restarts. Applicable to any solvated nanocluster system. [Read More →](/posts/gromacs-equilibration-production/) --- ### [Building pd4.ff — A Force Field File for the Pd₄ Cluster in fftool](/posts/pd4-ff/) **Date**: June 17, 2026 **Categories**: Molecular Dynamics Force Field **Tags**: #lammps #fftool #palladium #md-simulation #force-field #packmol 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 follows the same structure. The LJ parameters are identical between the two files — the differences lie entirely in the... [Read More →](/posts/pd4-ff/) --- ### [Building pd3.ff — A Force Field File for the Pd₃ Cluster in fftool](/posts/pd3-ff/) **Date**: June 17, 2026 **Categories**: Molecular Dynamics Force Field **Tags**: #lammps #fftool #palladium #md-simulation #force-field #packmol 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 clearly identified source. The goal is a file that can be dropped directly into an fftool workflow alongside opc.ff for... [Read More →](/posts/pd3-ff/) --- ### [Running a Pd3 Cluster in OPC Water: A Complete LAMMPS Simulation Guide](/posts/pd3-h2o-lmp/) **Date**: June 17, 2026 **Categories**: Molecular Dynamics HPC Palladium Solvation **Tags**: #LAMMPS #OPC #TIP4P #INTERFACE-FF #Pd3 #minimization #NPT #PARAM-Shakti #HPC 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 job submission. Written as a living debug log so others can skip the weeks of trial and... [Read More →](/posts/pd3-h2o-lmp/) --- ### [M.Tech Thesis CH](/posts/Thesis-Mtech/) **Date**: October 14, 2023 **Categories**: Book **Tags**: #thesis [Read More →](/posts/Thesis-Mtech/) --- ### [Installing GPU Driver](/posts/GPU_Driver_Installation/) **Date**: April 02, 2023 **Categories**: Drivers GPU **Tags**: #linux 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 “Additional Drivers” tab. Select the latest driver. In this case, nvidia-driver-470(proprietary, tested) “Apply changes” and Reboot. Open the terminal... [Read More →](/posts/GPU_Driver_Installation/) --- ### [Accessing HPC](/posts/accessing-hpc/) **Date**: March 22, 2023 **Categories**: software guidelines **Tags**: #tutorials 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 computer No extra instruction is required for the installation just leave everything to default. Logging in to your... [Read More →](/posts/accessing-hpc/) --- ### [Simulation of C atoms in LAMMPS](/posts/simulation_of_Carbon_Atoms/) **Date**: March 09, 2023 **Categories**: project C_atoms **Tags**: #tutorials 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 generated here in this sections, these examples are here only for a basic understanding of lammps. Avogadro first open... [Read More →](/posts/simulation_of_Carbon_Atoms/) --- ### [IOT Project Wifi Temp Sensor](/posts/wifi-temp-sensor/) **Date**: March 06, 2023 **Categories**: **Tags**: 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 hotspot qmel@123. Wait for few minutes when a device named “ESP-EAE289” get connected from the hotspot Go to setting of your hotspot... [Read More →](/posts/wifi-temp-sensor/) --- ### [Post Processing of the thermodynamics data using python code](/posts/post-processing/) **Date**: March 06, 2023 **Categories**: **Tags**: Post Processing There are lots of option available for analyzing the LAMMPS output data, out of many options few methods are illustrated here Using Python Script Plotting T,P,E,Rho Vs time Follow this github repository github for more details about the code. Here, sample code is given for the analysis of... [Read More →](/posts/post-processing/) --- ### [Generating Data file for LAMMPS](/posts/data-file/) **Date**: March 04, 2023 **Categories**: **Tags**: Data.Lammps Let’s create cyclohexylamine in a periodic box of dimensions 60*60*60 cubic angstrom. Step 01: Ligpargen Goto the Ligand parameter generator Ligpargen online server and draw molecule (cyclohexylamine) Now press convert to SMILES Leave everything as default and then press submit molecule Now wait for few minutes then download all... [Read More →](/posts/data-file/) --- ### [Videos and Graphs](/posts/Videos-and-Graphs/) **Date**: March 04, 2023 **Categories**: analysing_trajectories post_processing **Tags**: #videos Videos Agglomeration Graphs [Read More →](/posts/Videos-and-Graphs/) --- ### [Prerequisite](/posts/Prerequisite/) **Date**: March 04, 2023 **Categories**: **Tags**: Prerequisite First thing first, all the instructions you will read here are specifically for Linux based systems (Ubuntu 22.04) Operating system: It is recommended to use the latest version of Ubuntu from the official website. LAMMPS can also be installed on Windows but, to get full control of its features... [Read More →](/posts/Prerequisite/) --- ### [Writing Input script for LAMMPS](/posts/Input-file/) **Date**: March 04, 2023 **Categories**: **Tags**: Input.Lammps Requirements: To start with the following sections you need to have Lammps installed with following packages enabled: Copy of all option by running “ccmake ../cmake” in lammps/build directory. BUILD_MPI ON BUILD_OMP ON BUILD_TESTING ON CMAKE_POSITION_INDEPENDENT_COD ON Kokkos_ENABLE_COMPLEX_ALIGN ON Kokkos_ENABLE_DEPRECATED_CODE_ ON Kokkos_ENABLE_DEPRECATION_WARN ON Kokkos_ENABLE_IMPL_DESUL_ATOMI ON Kokkos_ENABLE_LAUNCH_COMPILER ON Kokkos_ENABLE_LIBDL ON Kokkos_ENABLE_SERIAL... [Read More →](/posts/Input-file/) ---