163 related articles for article (PubMed ID: 21317044)
1. Global energy minimization of alanine dipeptide via barrier function methods.
Ng KM; Solayappan M; Poh KL
Comput Biol Chem; 2011 Feb; 35(1):19-23. PubMed ID: 21317044
[TBL] [Abstract][Full Text] [Related]
2. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.
Okumura H
Phys Chem Chem Phys; 2011 Jan; 13(1):114-26. PubMed ID: 21038036
[TBL] [Abstract][Full Text] [Related]
3. Single-sweep methods for free energy calculations.
Maragliano L; Vanden-Eijnden E
J Chem Phys; 2008 May; 128(18):184110. PubMed ID: 18532802
[TBL] [Abstract][Full Text] [Related]
4. Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data.
Cruz V; Ramos J; Martínez-Salazar J
J Phys Chem B; 2011 Apr; 115(16):4880-6. PubMed ID: 21469661
[TBL] [Abstract][Full Text] [Related]
5. Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.
Bonomi M; Barducci A; Parrinello M
J Comput Chem; 2009 Aug; 30(11):1615-21. PubMed ID: 19421997
[TBL] [Abstract][Full Text] [Related]
6. Harmonic Fourier beads method for studying rare events on rugged energy surfaces.
Khavrutskii IV; Arora K; Brooks CL
J Chem Phys; 2006 Nov; 125(17):174108. PubMed ID: 17100430
[TBL] [Abstract][Full Text] [Related]
7. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.
Mackerell AD; Feig M; Brooks CL
J Comput Chem; 2004 Aug; 25(11):1400-15. PubMed ID: 15185334
[TBL] [Abstract][Full Text] [Related]
8. Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the alanine dipeptide.
Echenique P; Calvo I; Alonso JL
J Comput Chem; 2006 Nov; 27(14):1733-47. PubMed ID: 16900494
[TBL] [Abstract][Full Text] [Related]
9. Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide.
Ren W; Vanden-Eijnden E; Maragakis P; E W
J Chem Phys; 2005 Oct; 123(13):134109. PubMed ID: 16223277
[TBL] [Abstract][Full Text] [Related]
10. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Okumura H
J Chem Phys; 2008 Sep; 129(12):124116. PubMed ID: 19045015
[TBL] [Abstract][Full Text] [Related]
11. Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation.
Echenique P; Alonso JL
J Comput Chem; 2006 Jul; 27(10):1076-87. PubMed ID: 16685717
[TBL] [Abstract][Full Text] [Related]
12. An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide.
Freedman H; Truong TN
J Chem Phys; 2004 Dec; 121(24):12447-56. PubMed ID: 15606265
[TBL] [Abstract][Full Text] [Related]
13. Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.
Itoh SG; Okumura H; Okamoto Y
J Chem Phys; 2010 Apr; 132(13):134105. PubMed ID: 20387919
[TBL] [Abstract][Full Text] [Related]
14. The SAAP force field. A simple approach to a new all-atom protein force field by using single amino acid potential (SAAP) functions in various solvents.
Iwaoka M; Tomoda S
J Comput Chem; 2003 Jul; 24(10):1192-200. PubMed ID: 12820126
[TBL] [Abstract][Full Text] [Related]
15. Monte Carlo simulations of biomolecules: The MC module in CHARMM.
Hu J; Ma A; Dinner AR
J Comput Chem; 2006 Jan; 27(2):203-16. PubMed ID: 16323162
[TBL] [Abstract][Full Text] [Related]
16. Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra.
Kwac K; Lee KK; Han JB; Oh KI; Cho M
J Chem Phys; 2008 Mar; 128(10):105106. PubMed ID: 18345930
[TBL] [Abstract][Full Text] [Related]
17. Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment.
Jono R; Watanabe Y; Shimizu K; Terada T
J Comput Chem; 2010 Apr; 31(6):1168-75. PubMed ID: 19847783
[TBL] [Abstract][Full Text] [Related]
18. Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations.
van der Vaart A; Karplus M
J Chem Phys; 2007 Apr; 126(16):164106. PubMed ID: 17477588
[TBL] [Abstract][Full Text] [Related]
19. Periodic orbits in biological molecules: phase space structures and selectivity in alanine dipeptide.
Farantos SC
J Chem Phys; 2007 May; 126(17):175101. PubMed ID: 17492886
[TBL] [Abstract][Full Text] [Related]
20. From A to B in free energy space.
Branduardi D; Gervasio FL; Parrinello M
J Chem Phys; 2007 Feb; 126(5):054103. PubMed ID: 17302470
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
