Small Molecule Solvation Free Energy: Enhanced Conformational Sampling Using Expanded Ensemble Molecular Dynamics Simulation

2011 ◽  
Vol 7 (9) ◽  
pp. 2910-2918 ◽  
Author(s):  
Andrew S. Paluch ◽  
David L. Mobley ◽  
Edward J. Maginn
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Small Molecule ◽  
Solvation Free Energy ◽  
Dynamics Simulation ◽  
Conformational Sampling ◽  
Expanded Ensemble

Performance of molecular dynamics simulation for predicting of solvation free energy of neutral solutes in methanol

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Mohammad Emamian ◽  
Hedayat Azizpour ◽  
Hojatollah Moradi ◽  
Kamran Keynejad ◽  
Hossein Bahmanyar ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Solvation Free Energy ◽  
Summation Method ◽  
Dynamics Simulation ◽  
Experimental Result ◽  
Coefficient Of Determination ◽  
Solvation Model ◽  
The Difference

Abstract In this study, molecular dynamics simulation was applied for calculating solvation free energy of 16 solute molecules in methanol solvent. The thermodynamic integration method was used because it was possible to calculate the difference in free energy in any thermodynamic path. After comparing results for solvation free energy in different force fields, COMPASS force field was selected since it had the lowest error compared to experimental result. Group-based summation method was used to compute electrostatic and van der Waals forces at 298.15 K and 1 atm. The results of solvation free energy were obtained from molecular dynamics simulation and were compared to the results from Solvation Model Density (SMD) and Universal Continuum Solvation Model (denoted as SM8), which were obtained from other research works. Average square-root-error for molecular dynamics simulation, SMD and SM8 models were 0.096091, 0.595798, and 0.70649. Furthermore, the coefficient of determination (R 2) for molecular dynamics simulation was 0.9618, which shows higher accuracy of MD simulation for calculating solvation free energy comparing to two other models.

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile
Sign in / Sign up

Export Citation Format

Share Document