scholarly journals Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

2015 ◽  
Vol 7 (17) ◽  
pp. 2317-2331 ◽  
Author(s):  
Gautier Moroy ◽  
Olivier Sperandio ◽  
Shakti Rielland ◽  
Saurabh Khemka ◽  
Karen Druart ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Conformational Ensemble ◽  
Dynamics Simulations

scholarly journals Collective Mode Mining from Molecular Dynamics Simulations: A Comparative Approach

2018 ◽  
Vol 15 (03) ◽  
pp. 1850108 ◽  
Author(s):  
Vito Dario Camiola ◽  
Valentina Tozzini
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Normal Mode Analysis ◽  
Principal Component ◽  
Mode Analysis ◽  
Comparative Approach ◽  
Atomic Systems ◽  
Equilibrium Dynamics ◽  
Definition Of ◽  
Dynamics Simulations

The evaluation of collective modes is fundamental in the analysis of molecular dynamics simulations. Several methods are available to extract that information, i.e., normal mode analysis, principal component and spectral analysis of trajectories, basically differing by the quantity considered as the nodal one (frequency, amplitude, or pattern of displacement) and leading to the definition of different kinds of collective excitations and physical spectral observables. The different views converge in the harmonic regime and/or for homo-atomic systems. However, for anharmonic and out of equilibrium dynamics, different quantities bring different information, and only their comparison can give a complete view of the system behavior. To allow such a comparative analysis, we review and compare the different approaches, applying them in diverse combinations to two examples of physical relevance: graphene and fullerene C[Formula: see text].

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