2024-03-28T13:24:17Zhttps://www.tdx.cat/oai/requestoai:www.tdx.cat:10803/1250712024-03-15T10:57:24Zcom_10803_236col_10803_690278
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Multiscale molecular dynamics
Coarse-grained force-field
Free energy perturbation
Non-polar solvation free energy
Solvent accessible surface area
Collective variable
Chicken villin headpiece
Triforce
Exposed boundary
Dinámica molecular multiescala
Campos de fuerza de grano grueso
Perturbación de energía libre
Solvatación energía libre no-polar
Superficie accesible al disolvente
Variables colectiva
Expuestos límite
Development of a multiscale protocol for the study of energetics of protein dymanics
[Barcelona] :
Universitat Pompeu Fabra,
2013
Accés lliure
http://hdl.handle.net/10803/125071
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Drechsel, Nils Jan Daniel,
autor
Programa de doctorat en Biomedicina,
degree
1 recurs en línia (167 pàgines)
Tesi
Doctorat
Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut
2013
Universitat Pompeu Fabra. Departament de Ciències Experimentals i de la Salut
Tesis i dissertacions electròniques
Villà i Freixa, Jordi,
supervisor acadèmic
Dill, Ken A.,
supervisor acadèmic
TDX
Multiscale Molecular Dynamics is a popular trend in the field of computational chemistry and physics. Coarse-grained force-fields have been around for years, and used independently, but used cooperatively with all-atom force-fields combines their advantages and cancels their disadvantages. This seems to be the case, however, only when they are both compatible. In this thesis, a Multiscale Molecular Dynamics Protocol is introduced, based on earlier work by Benjamin Messer, Z. Fan, Arieh Warshel, and in other parts by Christopher Fennel and Ken Dill. The protocol consists of the following tool-set:
• A parametrization machinery that created a new coarse-grained force-field named AmberCG.
• A multiscale thermodynamic cycle utilized within a free energy perturbation context to cooperatively use the best of coarse-grained and all-atom force-fields.
• A collective variable that performs a linearization of the phase space to improve separation of product and reactant states.
• A new algorithm to calculate functional quantities on spheres bounded by complicated solvent accessible surface areas - which as a special case calculates the amount of solvent accessible surface area.
• A novel algorithm based on simple one dimensional Depth-Buffers, to identify atoms which actively form the boundary of the solvent accessible surface areas.
Executing the protocol involves the following steps:
1. Construction of a coarse-grained force-field, based on an all-atom force-field. This involves setting up coarse-grained potentials and optimization of their parameters against selected reference structures and conformations.
2. Parametrization of a solvation model which is compatible to the force-field.
3. Usage of the coarse-grained force-field to sample the conformational space of a reaction.
4. Correction of the coarse-grained results with an all-atom force-field.
5. Analysis of the results using appropriate collective coordinates.
6. Reiteration until accuracies are met.
Alternatively, instead of using the methods in the protocol, they
can be utilized stand-alone. They simplify calculations, thus provid-
ing speed-ups, while at the same time aiming to maintain or improve
accuracy. Of course, there is no free lunch, and often the methods will
include inaccuracies that exceed an acceptable threshold. However, the
multiscale protocol is meant to be seen as an iterative technique, in
which deficiency can be detected, and the protocol adjusted to restore
balance.
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