How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?

Villa, A, Fan, H, Wassenaar, T and Mark, AE (2007) How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?. Journal of Physical Chemistry B, 111 21: 6015-6025. doi:10.1021/jp068580v


Author Villa, A
Fan, H
Wassenaar, T
Mark, AE
Title How sensitive are nanosecond molecular dynamics simulations of proteins to changes in the force field?
Journal name Journal of Physical Chemistry B   Check publisher's open access policy
ISSN 1520-6106
Publication date 2007-05-10
Year available 2007
Sub-type Article (original research)
DOI 10.1021/jp068580v
Volume 111
Issue 21
Start page 6015
End page 6025
Total pages 11
Place of publication Washington
Publisher Amer Chemical Soc
Collection year 2008
Language eng
Subject C1
780103 Chemical sciences
Abstract The sensitivity of molecular dynamics simulations to variations in the force field has been examined in relation to a set of 36 structures corresponding to 31 proteins simulated by using different versions of the GROMOS force field. The three parameter sets used (43a1, 53a5, and 53a6) differ significantly in regard to the nonbonded parameters for polar functional groups and their ability to reproduce the correct solvation and partitioning behavior of small molecular analogues of the amino acid side chains. Despite the differences in the force field parameters no major differences could be detected in a wide range of structural properties such as the root-mean-square deviation from the experimental structure, radii of gyration, solvent accessible surface, secondary structure, or hydrogen bond propensities on a 5 to 10 ns time scale. The small differences that were observed correlated primarily with the presence of charged residues as opposed to residues that differed most between the parameter sets. The work highlights the variation that can be observed in nanosecond simulations of protein systems and implications of this for force field validation, as well as for the analysis of protein simulations in general.
Keyword Chemistry, Physical
Dna-binding Domain
3-dimensional Solution Structure
X-ray Crystallography
Helix-coil Transition
Side-chain Analogs
Crystal-structure
Condensed-phase
Terminal Domain
Nucleic-acids
Nmr Structure
Q-Index Code C1
Q-Index Status Confirmed Code

 
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Created: Tue, 19 Feb 2008, 03:17:26 EST