Comparison of implicit solvent models and force fields in molecular dynamics simulations of the PB1 domain

2011 ◽  
Vol 515 (4-6) ◽  
pp. 283-289 ◽  
Author(s):  
Mengchen Pu ◽  
Juan P. Garrahan ◽  
Jonathan D. Hirst
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Implicit Solvent ◽  
Solvent Models ◽  
Pb1 Domain ◽  
Dynamics Simulations ◽  
Implicit Solvent Models

scholarly journals Implicit solvent models fail to reproduce secondary structures of de novo designed peptides

2021 ◽  
Author(s):  
Eric Lang ◽  
Emily Baker ◽  
Derek Woolfson ◽  
Adrian Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Secondary Structure ◽  
Molecular Dynamics Simulations ◽  
De Novo ◽  
Secondary Structures ◽  
Implicit Solvent ◽  
Helical Peptides ◽  
Solvent Models ◽  
Dynamics Simulations ◽  
Implicit Solvent Models

We test a range of standard implicit solvent models and protein forcefields for a set of 5 experimentally characterized, designed α-helical peptides. 65 combinations of forcefield and implicit solvent models are evaluated in >800 µs of molecular dynamics simulations. The data show that implicit solvent models generally fail to reproduce the experimentally observed secondary structure content, and none performs well for all 5 peptides. The results show that these models are not usefully predictive.

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