SMOG extensions

Source Code Extensions to Gromacs for SMOG and SBMs

Note: no source code modifications are necessary for the default SMOG forcefield with Lennard-Jones contact interactions.

Contents

  1. Downloads
  2. MDfit
  3. Gaussian contact potentials
  4. Scripts
  5. Non-standard forcefield extensions

Downloads

The source code extensions are provided as fully functional Gromacs distributions. Download the relevant source distribution and compile as you would any Gromacs distribution, nothing special is required at compile time. For your convenience the extended distributions are linked here. See below for user guides and implementation details for the different extensions.

MDfit

MDfit is a computational methodology that allows you to incorporate information from x-ray crystallography, cryo-EM and biochemical studies in order to prepare atomic models for these configurations. The MDfit method starts with a structure-based model (such as those provided by the SMOG server). Details and tutorial are located here.

Gaussian contact potentials

The Gaussian contact potentials bring freedom of creativity to the modeller by releasing them from the chains of the Lennard-Jones excluded volume. Variable numbers of Gaussian wells can be positioned with variable excluded volume size. Details and examples are located here.

Scripts

  • g_kuh - calculates Q, the fraction of native contacts for a trajectory (.xtc). Part of the Gaussian contact extension: tar.gz.

Non-standard forcefield extensions

One of the reasons for making the SMOG class of models publicly accessible is so that there can be a common framework for studying complex systems. This means that we encourage users to perturb and extend the standard SMOG models in order to study the effects of a wide range of interactions. Here we provide descriptions and scripts necessary to utilize user-contributed variants of SMOG models.
  • Non-specific magnesium ion parameters: Hayes et al. (2014) Biophysical Journal more information
  • Non-specific magnesium-RNA interaction model with generalized Manning model of KCl: Hayes et al. (2015) Phys. Rev. Lett. more information

Page last edited on 3/13/15.

Please direct questions and comments to info@smog-server.org.
Page created and maintained by Jeff Noel and Paul Whitford