The improvement of the algorithm for order parameter calculation (S2) from molecular dynamics simulation using the correlation motion function.
The generalized order parameter, S2, calculated from MD simulation trajectory using time-dependent internal Correlation Motion Function (CMF) agrees well with NMR derived S2 processed with the extended model-free analysis approach. However, the former lies considerably lower comparing to simple model-free derived data from NMR experiments. In the present study we analyze possible reasons of such disagreement. In the general case we propose to use preexponential factors from expression for internal CMF rather than ordinary S2 values. Particularly, in case of the simple model-free S(2) experimental values we suggest comparing them with S2(eff)=1+S2-Sf2 computed from MD simulation data. We show that the S2(eff) values are in a good agreement with NMR derived S2 values obtained using the simple model-free analysis.
Dubyna
V M
VM
Institute of Molecular Biology and Genetics, 150 Akad. Zabolotny Str, Kyiv-143, 03143, Ukraine. vdubyna@univ.kiev.ua
Kovalskyy
D B
DB
Ivanova
O S
OS
Kornelyuk
A I
AI
D000465:Algorithms; D009682:Magnetic Resonance Spectroscopy; D010455:Peptides / Q000737:chemistry*
D010455:Peptides