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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS.

Kutzner C, Czub J, Grubmüller H - J Chem Theory Comput (2011)

Bottom Line: In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation.A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package.Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

View Article: PubMed Central - PubMed

Affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

ABSTRACT
We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

No MeSH data available.


Gaussian functions gn centered at nΔx for a slab distance Δx = 1.5 nm and n ≥ −2. Gaussian function g0 is highlighted in bold; the dashed line depicts the sum of the shown Gaussian functions.
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fig3: Gaussian functions gn centered at nΔx for a slab distance Δx = 1.5 nm and n ≥ −2. Gaussian function g0 is highlighted in bold; the dashed line depicts the sum of the shown Gaussian functions.

Mentions: A most convenient choice is σ = 0.7Δx andwhich yields a nearly constant sum, essentially independent of xi (dashed line in Figure 3), i.e.,with /ε(xi)/ < 1.3 × 10−4. This choice also implies that the individual contributions to the force from the slabs add up to unity such that no further normalization is required.


Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS.

Kutzner C, Czub J, Grubmüller H - J Chem Theory Comput (2011)

Gaussian functions gn centered at nΔx for a slab distance Δx = 1.5 nm and n ≥ −2. Gaussian function g0 is highlighted in bold; the dashed line depicts the sum of the shown Gaussian functions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091370&req=5

fig3: Gaussian functions gn centered at nΔx for a slab distance Δx = 1.5 nm and n ≥ −2. Gaussian function g0 is highlighted in bold; the dashed line depicts the sum of the shown Gaussian functions.
Mentions: A most convenient choice is σ = 0.7Δx andwhich yields a nearly constant sum, essentially independent of xi (dashed line in Figure 3), i.e.,with /ε(xi)/ < 1.3 × 10−4. This choice also implies that the individual contributions to the force from the slabs add up to unity such that no further normalization is required.

Bottom Line: In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation.A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package.Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

View Article: PubMed Central - PubMed

Affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

ABSTRACT
We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

No MeSH data available.