Software

As we are a computational chemistry group, we use a lot of software and write quite a few lines for our specific purposes. Most of this software in the public domain available, but some only to academic institutions.

 

For our Molecular Dynamics simulations we use the GROMACS hardware, consisting of parallel computers connected to a workstation, and the GROMACS software package which is free for non-commercial use and runs on various types of computers.

 

 

Some features of the software:

1. Standard Molecular Dynamics simulations
2. Energy minimizations
3. NMR Refinement using NOE data
4. High performance due to well optimized code and smart algorithms

5. Automatic topology generation from a building block library

6. Flexible force field usage
7. Non-Equilibrium Molecular Dynamics
8. Many analysis tools
9. Many pre-processing tools
10. A simple trajectory viewer  

More info and instruction of how to download this software on the:

GROMACS home page

Other useful info from the MDgroup:

Coarse grained forcefield for lipid simulations

 

Concoord is a method to generate protein structures around a known conformation. Principal component analyses of Molecular Dynamics (MD) simulations of proteins have indicated that collective degrees of freedom dominate protein conformational fluctuations. These large-scale collective motions have been shown essential to protein function in a number of cases. The notion that internal constraints and other configurational barriers restrict protein dynamics to a limited number of collective degrees of freedom has led to the design of the CONCOORD method to predict these modes without doing explicit, more CPU intensive, MD simulations.

 

 

The input structure is scanned for interatomic interactions, from which upper and lower distance limits are derived. Starting from random coordinates, corrections are iteratively applied until all distance bounds are fulfilled. Differences between generated structures have been shown to be similar to fluctuations observed in Molecular Dynamics simulations. Go to the Concoord page for more information.

 

Dyndom is a program that determines protein domains, hinge axes and amino acid residues involved in the hinge bending motion. It requires two conformations to perform this task. It is fully automated and applicable to multi-domain proteins.

More info and from the DynDom page from where you can also download the source.