The goal of this tutorial is the simulation of a small protein and one of its mutants. The protein, called chignolin, is a designed protein of 10 amino acid residues that, when synthesized, shows a stable 3D structure in aqueous solution (see S. Honda, K. Yamasaki, Y. Sawada and H. Morii. 10 Residue Folded Peptide Designed by Segment Statistics. Structure 12, 1507–1518 (2004) [Link]). The size of the protein means that molecular dynamics simulations of reasonable length can be carried out without using excessive computer resources.
This tutorial is more advanced than some of the others in the pDynamo distribution as a detailed guide of how to perform each of the tasks is not given. Instead readers are encouraged to find their own solutions.
The steps in the tutorial are given below whereas programs
implementing possible solutions to each of the tasks may be found in the