Let's get honest about sampling

J Comput Aided Mol Des. 2012 Jan;26(1):93-5. doi: 10.1007/s10822-011-9497-y. Epub 2011 Nov 24.

Abstract

Molecular simulations see widespread and increasing use in computation and molecular design, especially within the area of molecular simulations applied to biomolecular binding and interactions, our focus here. However, force field accuracy remains a concern for many practitioners, and it is often not clear what level of accuracy is really needed for payoffs in a discovery setting. Here, I argue that despite limitations of today's force fields, current simulation tools and force fields now provide the potential for real benefits in a variety of applications. However, these same tools also provide irreproducible results which are often poorly interpreted. Continued progress in the field requires more honesty in assessment and care in evaluation of simulation results, especially with respect to convergence.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computer Simulation*
  • Humans
  • Ligands
  • Models, Molecular*
  • Molecular Conformation
  • Protein Binding

Substances

  • Ligands