GROMACS Tutorial

Step One: Introduction

This tutorial assumes that the reader is familiar with the concept of virtual sites and all the information contained in the GROMACS manual, sections 4.7 and 5.2.2. If not, please familiarize yourself with this information. In this tutorial, instructions will be provided to build a simple linear molecule, carbon dioxide (CO2). One cannot effectively build this molecule in the traditional sense, as there are algorithmic reasons why an angle of 180° is not stable during a simulation.

To summarize a few key points regarding virtual sites:

  1. Virtual sites have no mass
  2. Virtual sites can have LJ and charge interactions
  3. Forces acting on virtual sites are projected onto constructing mass centers
  4. The positions of virtual sites are not updated via integration, they are constructed from the updated positions of the mass centers

Therefore, we approach this issue in the following way. The CO2 molecule will be constructed from two massive atoms with no charges or van der Waals parameters. The C and O atoms are converted to virtual sites, with their positions constructed from the positions of the massive atoms.

There are a few things to be considered when constructing a molecule in this way:

  1. The molecule must have the same mass as if it were constructed of normal atoms
  2. The molecule must have the same moment of inertia as if it were constructed of normal atoms

These issues will be addressed when considering the topology.

Back: Introduction Next: The Topology

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