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    Calculating Free Energies Using Adaptive Biasing Force Method

    Uploaded by

    Amin Sagar
    This document discusses methods for calculating free energies using the Adaptive Biasing Force (ABF) method. It begins with an introduction to free energy and challenges with traditional calculations. It then describes the ABF method, which applies a biasing force to more completely explore phase space and converge free energy calculations faster than traditional thermodynamics integration. The document presents a numerical example comparing ABF to thermodynamics integration for a simple potential and finds ABF results match the expected potential. It concludes ABF is easier to implement and converges free energy calculations faster.

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    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd

    Calculating Free Energies Using Adaptive Biasing Force Method

    Uploaded by

    Amin Sagar
    76 views14 pages
    This document discusses methods for calculating free energies using the Adaptive Biasing Force (ABF) method. It begins with an introduction to free energy and challenges with traditional calculations. It then describes the ABF method, which applies a biasing force to more completely explore phase space and converge free energy calculations faster than traditional thermodynamics integration. The document presents a numerical example comparing ABF to thermodynamics integration for a simple potential and finds ABF results match the expected potential. It concludes ABF is easier to implement and converges free energy calculations faster.

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    This document discusses methods for calculating free energies using the Adaptive Biasing Force (ABF) method. It begins with an introduction to free energy and challenges with traditional calculations. It then describes the ABF method, which applies a biasing force to more completely explore phase space and converge free energy calculations faster than traditional thermodynamics integration. The document presents a numerical example comparing ABF to thermodynamics integration for a simple potential and finds ABF results match the expected potential. It concludes ABF is easier to implement and converges free energy calculations faster.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    76 views14 pages

    Calculating Free Energies Using Adaptive Biasing Force Method

    Uploaded by

    Amin Sagar
    This document discusses methods for calculating free energies using the Adaptive Biasing Force (ABF) method. It begins with an introduction to free energy and challenges with traditional calculations. It then describes the ABF method, which applies a biasing force to more completely explore phase space and converge free energy calculations faster than traditional thermodynamics integration. The document presents a numerical example comparing ABF to thermodynamics integration for a simple potential and finds ABF results match the expected potential. It concludes ABF is easier to implement and converges free energy calculations faster.

    Copyright:

    Attribution Non-Commercial (BY-NC)
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 14

    Calculating free energies

    using Adaptive biasing force


    method

    Joanne Chiu
    Department of Mechanical Engineering,
    Stanford
    2009/6/3
    Introduction
    Free Energy
    Determination of the most stable
    conformation
    Computing the reaction rate
    Determination of probabilities at equilibrium
    First step in building a course grained model
    of protein
    Examples
    Fuel Cell reaction rate
    Protein-ligand binding and ion partitioning
    across the cell membrane

    2009/6/3
    However
    Free Energy Calculation
    Needs first and second derivatives of the
    order parameter with respect to Cartesian
    coordinates
    Expensive computation and long
    calculation time
    Accuracy

    2009/6/3
    Thermodynamics Integration
    2009/6/3

    o
    c
    c

    c
    c
    =
    =

    }
    J
    kT
    U
    d
    dA
    dq q e kT A
    q U
    ln
    ) (
    )) ( ( ln ) (
    ) (
    Lecture 08
    Assume there is no momentum in the
    Hamiltonian of the system.
    J is already the first derivative of q, thus
    we need to get the second derivative of
    q.
    Adaptive Biasing Force
    Based on computing the mean force
    on
    A free computation using the equation:
    2009/6/3

    ( )
    2
    1
    1
    ) (
    |
    |
    .
    |

    \
    |
    c
    c
    =
    =

    k
    k
    k
    q m
    m
    m
    dt
    d
    d
    dA


    wher
    e
    ( )
    i i
    i
    q m
    dt
    d
    dq
    dU
    =
    The governing equation of
    motion:
    Adaptive Biasing Force (Cont.)
    Applying a biasing force
    2009/6/3
    V
    b
    F

    Take a long time to go


    over the energy
    barrier
    Much easier to reach
    another state
    Local minimum
    Global minimum
    Numerical Results
    2009/6/3
    Glycophorin A: key interactions
    between the two helical segments



    Simulation Setup
    Two molecules connected with a
    spring and the potential is given by:




    Because there is no long range force,
    free energy should be the same as
    potential energy.
    2009/6/3
    ( )
    2
    2 1 0
    2
    x x
    k
    U =
    1
    x
    2
    x
    Free energy calculation
    Thermodynamics Integration
    2009/6/3
    ( )
    ( )
    ( )
    ( )
    ( )
    ( )
    1 2
    2
    1 2
    2
    2
    1 2
    2
    1 2
    0
    2
    1 2
    0
    2
    1 2
    0
    0
    ) (
    ) (
    ln ) (
    ln ) (
    x x x
    dq e e
    dq x x x e e
    dx
    x dA
    dx e e kT x A
    dx x x x e kT x A
    x x x
    U
    x x x
    U
    x x x
    U
    U
    + =
    +
    =
    =
    + =
    }
    }
    }
    }
    +

    o
    o
    o
    o
    |
    |
    o
    |
    |
    o
    |
    |
    |
    Replace
    impulse by
    Gaussian
    distribution
    Thermodynamics Integration







    Calculated free energy (U) will be slightly
    different from the potential energy(U
    0
    ).

    2009/6/3
    ( )
    ( )
    ( )
    2
    1 2 0
    2
    2
    2
    ln ) (
    ln ) (
    2
    1 2 0
    2
    1 2
    0
    x x x U U
    dx e kT x A
    dx e e kT x A
    x x x U
    x x x
    U
    + + =
    =
    =
    }
    }
    |
    .
    |

    \
    |
    + +
    +

    o
    o
    |
    o
    |
    |
    Free energy calculation
    Adaptive Biasing Force
    2009/6/3
    ( ) ( ) ( )
    ( )
    1 2 1 2
    2
    2
    2
    1
    2
    1
    1 2
    1 2 1 2
    2
    1
    2
    1 ) (
    2
    1
    ) (
    F F v v
    dt
    d
    d
    x dA
    x x q m
    m
    v v m
    dt
    d
    m
    dt
    d
    d
    x dA
    v v x x
    k
    k
    k
    =
    |
    .
    |

    \
    |
    =
    =
    |
    |
    .
    |

    \
    |
    c
    c
    +
    |
    |
    .
    |

    \
    |
    c
    c
    =
    |
    |
    .
    |

    \
    |
    c
    c
    =
    = =
    = =

    Assume the mass of two particles are 1:


    0 1 2 3 4 5 6
    0
    0.5
    1
    1.5
    2
    2.5
    3
    3.5
    4
    4.5
    Reaction Coordinate
    E
    n
    e
    r
    g
    y


    Potential
    ABF
    ABF simulation result
    2009/6/3
    ( )
    2
    2 1 0
    2
    1
    x x U =
    2
    1
    = x 5
    2
    = x
    Potential
    Match
    Conclusion
    ABF is easier to implement and only
    need to evaluate the first derivatives
    and the derivatives with time.
    With applying biasing force, the phase
    space can be explored more
    completely.
    The free energy converges faster than
    Thermodynamics Integrator.
    2009/6/3
    Future Work
    Comparing the simulation results of TI
    and ABF.
    Changing the potential to create a low/
    relatively high energy barrier and
    comparing the results .
    Adding biasing force to see if the
    accuracy is improved.
    Adding long range force (more
    molecules) to calculate the new free
    energy by applying both methods.
    2009/6/3

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