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Assessing equilibration and convergence in biomolecular simulations.

Abstract:

If molecular dynamics simulations are used to characterize the folding of peptides or proteins, a wide range of conformational states needs to be sampled. This study reports an analysis of peptide simulations to identify the best methods for assessing equilibration and sampling in these systems where there is significant conformational disorder. Four trajectories of a beta peptide in methanol and four trajectories of an alpha peptide in water, each of 5 ns in length, have been studied. Compar...

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Publication status:
Published

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Publisher copy:
10.1002/prot.10144

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Institution:
University of Oxford
Department:
Oxford, MPLS, Chemistry, Inorganic Chemistry
Role:
Author
Journal:
Proteins
Volume:
48
Issue:
3
Pages:
487-496
Publication date:
2002-08-05
DOI:
EISSN:
1097-0134
ISSN:
0887-3585
URN:
uuid:883b40cc-63e0-4cbb-a1eb-8f8fd960d0bf
Source identifiers:
32144
Local pid:
pubs:32144

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