期刊
JOURNAL OF BIOMOLECULAR NMR
卷 60, 期 2-3, 页码 169-187出版社
SPRINGER
DOI: 10.1007/s10858-014-9866-7
关键词
Structure refinement; Nuclear magnetic resonance; Force field; Conformational dynamics; Statistical mechanics
资金
- National Center of Competence in Research (NCCR) in Structural Biology
- Swiss National Science Foundation [200020-137827]
- European Research Council [228076]
- German Research Foundation (DFG) within the Cluster of Excellence in Simulation Technology at the University of Stuttgart [EXC 310/1]
A method is described that allows experimental order parameters to be enforced as a time-averaged quantity in molecular dynamics simulations. The two parameters that characterize time-averaged restraining, the memory relaxation time and the weight of the restraining potential energy term in the potential energy function used in the simulation, are systematically investigated based on two model systems, a vector with one end restrained in space and a pentapeptide. For the latter it is shown that the backbone N-H order parameter of individual residues can be enforced such that the spatial fluctuations of quantities depending on atomic coordinates are not significantly perturbed. The applicability to realistic systems is illustrated for the B3 domain of protein G in aqueous solution.
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