+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Free energy calculations for molecular solids using GROMACS



Free energy calculations for molecular solids using GROMACS



Journal of Chemical Physics 139(3): 034104



In this work, we describe a procedure to evaluate the free energy of molecular solids with the GROMACS molecular dynamics package. The free energy is calculated using the Einstein molecule method that can be regarded as a small modification of the Einstein crystal method. Here, the position and orientation of the molecules is fixed by using an Einstein field that binds with harmonic springs at least three non-collinear atoms (or points of the molecule) to their reference positions. The validity of the Einstein field is tested by performing free-energy calculations of methanol, water (ice), and patchy colloids molecular solids. The free energies calculated with GROMACS show a very good agreement with those obtained using Monte Carlo and with previously published results.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 053299022

Download citation: RISBibTeXText

PMID: 23883007

DOI: 10.1063/1.4812362


Related references

Note: Free energy calculations for atomic solids through the Einstein crystal/molecule methodology using GROMACS and LAMMPS. Journal of Chemical Physics 137(14): 146101, 2012

A Python tool to set up relative free energy calculations in GROMACS. Journal of Computer-Aided Molecular Design 29(11): 1007-1014, 2015

Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations. Journal of Physical Chemistry. B 119(3): 810-823, 2015

Free-energy calculations in solids from first-principles molecular dynamics: Vacancy formation in sodium. Physical Review. B Condensed Matter 51(1): 117-128, 1995

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations. Journal of Chemical Theory and Computation 6(9): 2559-2565, 2010

Relative binding free energy calculations of inhibitors to two mutants (Glu46----Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches. Protein Engineering 4(3): 233-243, 1991

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins 16(3): 226-245, 1993

Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations. Journal of Chemical Physics 136(14): 145101, 2012

Relative binding free energy calculations of inhibitors to two mutants glu46 ala46 and glu46 glu46 of rnase t1 using molecular dynamics free energy perturbation approaches. Protein Engineering 4(3): 233-244, 1991

Molecular dynamics and free energy perturbation calculations What role do they play in computer-assisted molecular design. FASEB Journal 9(6): A1253, 1995

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry 48(2): 399-414, 2009

Exploring the molecular basis of dsRNA recognition by Mss116p using molecular dynamics simulations and free-energy calculations. Langmuir 29(35): 11135-11144, 2013

Discovery and optimization of triazine derivatives as ROCK1 inhibitors: molecular docking, molecular dynamics simulations and free energy calculations. Molecular Biosystems 9(3): 361-374, 2013

Molecular recognition in a diverse set of protein-ligand interactions studied with molecular dynamics simulations and end-point free energy calculations. Journal of Chemical Information and Modeling 53(10): 2659-2670, 2013