Recent development and application of constant pH molecular dynamics
نویسندگان
چکیده
منابع مشابه
Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics
An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038-2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with current standard constant pH molecular dynamics...
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pH is an important parameter in condensed-phase systems, because it determines the protonation state of titratable groups and thus influences the structure, dynamics, and function of molecules in solution. In most force field simulation protocols, however, the protonation state of a system (rather than its pH) is kept fixed and cannot adapt to changes of the local environment. Here, we present ...
متن کاملMolecular Dynamics Simulation of Potassium Chloride Melting (II. Constant Volume and Constant Pressure Simulation of Filled System)
We have used a simple ionic potential to simulate the melting of KCI pseudo-infinite crystal. Two MD simulations, one with constant Volume and the other with constant pressure condition are performed. These results are compared with the previous micro-sample simulation results. In the constant volume simulation the melting temperature increase substantially with increasing pressure. A method fo...
متن کاملConstant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method
A computational method is developed to carry out explicit solvent simulations of complex molecular systems under conditions of constant pH. In constant-pH simulations, preidentified ionizable sites are allowed to spontaneously protonate and deprotonate as a function of time in response to the environment and the imposed pH. The method, based on a hybrid scheme originally proposed by H. A. Stern...
متن کاملConstant-pH molecular dynamics using continuous titration coordinates.
In this work, we explore the question of whether pK(a) calculations based on a microscopic description of the protein and a macroscopic description of the solvent can be implemented to examine conformationally dependent proton shifts in proteins. To this end, we introduce a new method for performing constant-pH molecular dynamics (PHMD) simulations utilizing the generalized Born implicit solven...
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ژورنال
عنوان ژورنال: Molecular Simulation
سال: 2014
ISSN: 0892-7022,1029-0435
DOI: 10.1080/08927022.2014.907492