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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

Authors


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Institution:
University of Oxford
Division:
MPLS
Department:
Chemistry
Sub department:
Inorganic Chemistry
Role:
Author
Journal:
Proteins
Volume:
48
Issue:
3
Pages:
487-496
Publication date:
2002-08-01
DOI:
EISSN:
1097-0134
ISSN:
0887-3585
Source identifiers:
32144
Language:
English
Keywords:
Pubs id:
pubs:32144
UUID:
uuid:883b40cc-63e0-4cbb-a1eb-8f8fd960d0bf
Local pid:
pubs:32144
Deposit date:
2012-12-19

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