Running simulations with other programs NAMD The following steps should allow for CGenFF to be used with NAMD: Download and unpack the latest CHARMM force field distribution Overwrite the main CGenFF topology and parameter files downladed in the previous step with the CGenFF version that is compatible with the toppar file(s) you got out of the CGenFF program […]
QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations. This website contains all information on how to install and use QuickFF. A detailed description of the methodology used by QuickFF to derive the force fields can be found in the corresponding papers. QuickFF literature […]
MDAnalysis documentation¶ Release: 0.19.2 Date: Nov 08, 2018 MDAnalysis (www.mdanalysis.org) is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, Amber, NAMD, LAMMPS, DL_POLY and other packages; it also reads other formats (e.g., PDB files and XYZ format trajectories; see Table of supported coordinate formats and Table of Supported Topology Formats for the full lists). It can write most of these formats, too, together with atom selections […]
GPUs are getting faster and faster every day can we use them to speed up our molecular dynamics simulations let’s find out [Music] hello and welcome to this video on molecular dynamics on GPU Maha dynamic simulations are computationally expensive at least for most systems that we are interested in this makes it very challenging […]
This online webinar shared an introduction to Molecular Dynamics (MD) simulations as well as explored some of the basic features and capabilities of LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator), a classical MD code. MD simulation programs are often used in the study of materials and can help researchers gain insight about properties on an atomic […]
In this video I give a short introduction to the LAMMPS simulation package. I will explain how LAMMPS can help you to run your molecular dynamics simulations faster and easier. I will also run a simple simulation with LAMMPS. The example LAMMPS input file can be found here:
This is a 5 minutes introduction to molecular dynamics simulation. Tools to generate initial state for your system: – LAMMPS lattice command: This command creates a 2D or 3D lattice. It supports a number of lattice types.
Introduce the basics of the molecular dynamics method to simulate the dynamics of the atoms according to time. Relevant research papers can be found at: http://www.lab-paris.com