Molecular dynamics simulation of the phase behavior of lamellar amphiphilic model systems

2003 ◽  
Vol 119 (17) ◽  
pp. 9308-9320 ◽  
Author(s):  
Hongxia Guo ◽  
Kurt Kremer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Phase Behavior ◽  
Model Systems ◽  
Dynamics Simulation

scholarly journals Molecular Dynamics Simulation of Phase Behavior in a Bolaamphiphilic Solution

2015 ◽  
Vol 10 (0) ◽  
pp. 3401029-3401029 ◽  
Author(s):  
Susumu FUJIWARA ◽  
Takumi MIYATA ◽  
Masato HASHIMOTO ◽  
Yuichi TAMURA ◽  
Hiroaki NAKAMURA ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Phase Behavior ◽  
Dynamics Simulation

Molecular dynamics simulation for phase behavior of amphiphilic solution

2011 ◽  
Vol 182 (1) ◽  
pp. 192-194 ◽  
Author(s):  
Susumu Fujiwara ◽  
Daiki Funaoka ◽  
Takashi Itoh ◽  
Masato Hashimoto
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Phase Behavior ◽  
Dynamics Simulation

scholarly journals Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
A Priori ◽  
Model Systems ◽  
Dynamics Simulation ◽  
High Mass ◽  
Mean Square ◽  
Dynamics Simulations

ABSTRACTPredicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2for Cγ, when the sampling was done, for each of these proteins, over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations using AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive toa prioriprediction of crystallographic B-factors of a folded globular protein.

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