Zobrazeno 1 - 10
of 17
pro vyhledávání: '"Anna-Pitschna E. Kunz"'
Publikováno v:
Molecular Physics
Simulation of the folding equilibrium of a polypeptide in solution is a computational challenge. Standard molecular dynamics (MD) simulations of such systems cover hundreds of nanoseconds, which is barely sufficient to obtain converged ensemble avera
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e5dcf714e6f2821f671187ed7fd86a8
https://doi.org/10.1080/00268976.2011.650716
https://doi.org/10.1080/00268976.2011.650716
Publikováno v:
ChemPhysChem
A method for conformational Boltzmann sampling of loops in proteins in aqueous solution is presented that is based on adiabatic decoupling molecular dynamics (MD) simulation with temperature or force scaling. To illustrate the enhanced sampling, the
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::53747cbb41fb6ce3c99dc4449d614c59
https://doi.org/10.1002/cphc.201100305
https://doi.org/10.1002/cphc.201100305
Publikováno v:
The Journal of Physical Chemistry A. 113:11570-11579
A new charge-on-spring (COS) model for water is introduced (COS/D). It includes a sublinear dependence of the induced dipole on the electric field for large field strength to include the effect of hyperpolarizability by damping the polarizability. On
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::812db114293741ad6781f0ecc5467a57
https://doi.org/10.1021/jp903164s
https://doi.org/10.1021/jp903164s
Publikováno v:
ChemPhysChem. 8:162-169
Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected b
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8957a60075307cd95ff44d1a4ec61869
https://doi.org/10.1002/cphc.200600527
https://doi.org/10.1002/cphc.200600527
Publikováno v:
Journal of Chemical Theory and Computation
Methodology to compute the relative static dielectric permittivity and dielectric relaxation time of molecular liquids is reviewed and explicit formulas are given for the external field method in the case of simulations using a spherical cutoff, in w
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a5652c47060eb1a50713b9a208cca017
https://pubmed.ncbi.nlm.nih.gov/26610137
https://pubmed.ncbi.nlm.nih.gov/26610137
Publikováno v:
The Journal of Physical Chemistry B. 110:8488-8498
A method to enhance sampling of rare events is presented. It makes use of distance or dihedral-angle restraints to overcome an energy barrier separating two metastable states or to stabilize a transition state between the two metastable states. In or
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::19b78c7b4326cc7a78b6efc78aa8a2fa
https://doi.org/10.1021/jp0604948
https://doi.org/10.1021/jp0604948
Autor:
Sereina Riniker, Jane R. Allison, Daan P. Geerke, Nathan Schmid, Philippe H. Hünenberger, Bruno A. C. Horta, Wilfred F. van Gunsteren, Anna-Pitschna E. Kunz
Publikováno v:
Journal of Computational Chemistry, 33(3), 340-353. John Wiley and Sons Inc.
Kunz, A P E, Allison, J R, Geerke, D P, Horta, B A C, Hünenberger, P H, Riniker, S, Schmid, N & van Gunsteren, W F 2012, ' New functionalities in the GROMOS biomolecular simulation software ', Journal of Computational Chemistry, vol. 33, no. 3, pp. 340-353 . https://doi.org/10.1002/jcc.21954
Journal of Computational Chemistry
Kunz, A P E, Allison, J R, Geerke, D P, Horta, B A C, Hünenberger, P H, Riniker, S, Schmid, N & van Gunsteren, W F 2012, ' New functionalities in the GROMOS biomolecular simulation software ', Journal of Computational Chemistry, vol. 33, no. 3, pp. 340-353 . https://doi.org/10.1002/jcc.21954
Journal of Computational Chemistry
Since the most recent description of the functionalities of the GROMOS software for biomolecular simulation in 2005 many new functions have been implemented. In this article, the new functionalities that involve modified forces in a molecular dynamic
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a8375d6df00710d43bcf8ea74669dde2
https://research.vu.nl/en/publications/e01887b9-4258-41aa-b591-18252e243514
https://research.vu.nl/en/publications/e01887b9-4258-41aa-b591-18252e243514
Publikováno v:
The Journal of Physical Chemistry B
Three methods to enhance the configurational sampling of ions in aqueous solution, temperature and Hamiltonian replica exchange and adiabatic decoupling with translational temperature scaling, were compared for a system of CaSO(4) in water. It took 1
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b2907667374ae243d0f40efc59a36c89
Autor:
Anna-Pitschna E. Kunz, Jožica Dolenc, Jane R. Allison, Nathan Schmid, Wilfred F. van Gunsteren, Andreas P. Eichenberger
Publikováno v:
Journal of Biomolecular NMR, 51 (3)
Journal of Biomolecular NMR
Journal of Biomolecular NMR
Journal of Biomolecular NMR, 51 (3)
ISSN:0925-2738
ISSN:1573-5001
ISSN:0925-2738
ISSN:1573-5001
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf246a792c291d5556c221ced8cf53a5
https://pubmed.ncbi.nlm.nih.gov/21858640
https://pubmed.ncbi.nlm.nih.gov/21858640
Publikováno v:
Molecular Physics
A one-site and a five-site polarizable model for liquid carbon tetrachloride (CCl4) is presented. They are based on a non-polarizable model consisting of five van der Waals sites not carrying any partial charges. In the one-site model, a charge on a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f05ea8d90d932b5b26480e9c38e24e87