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    • 8. 发明申请
    • SELF-GUIDED MOLECULAR DYNAMICS SIMULATION FOR EFFICIENT CONFORMATIONAL SEARCH
    • 自我指导分子动力学模拟有效的一致性搜索
    • WO0010067A2
    • 2000-02-24
    • PCT/US9918302
    • 1999-08-13
    • UNIV GEORGETOWNWU XIONG WUWANG SHAOMENG
    • WU XIONG-WUWANG SHAOMENG
    • G06F17/50G06F19/16G06F
    • G06F19/16
    • A method of forming a generated conformation of a molecular system comprising generating a molecular dynamics trajectory of said molecular system, wherein said trajectory is initiated by assigning to each atom in said molecular system a set of initial parameters comprising an initial velocity vector and an initial conformation wherein each atom in said molecular system is disposed in an initial position, and wherein said molecular dynamics trajectory is propagated by a computational procedure comprising: (a) calculating a current force exerted on each atom (i) by calculating a derivative of an energy function describing interactions between said atom (i) and other atoms in said molecule; (b) determining a guiding force gi describing an average along a portion of said trajectory of a force exerted on said atom (i); (c) determining a current position and velocity of said atom (i) by ajusting said previous position and velocity according to the equation miai = fi, wherein mi is the mass of atom (i), ai is an acceleration of atom (i) and fi is a force obtained by adding said current force calculated in (a) and said guiding force determined in (b); (d) replacing said previous position and velocity of said atom (i) with said current position and velocity of said atom (i); (e) repeating steps (a) to (d) for one or more iterations to generate said trajectory; and (f) forming said generated conformation by disposing the atoms of said molecule in respective current positions obtained during a given iteration; and processing said generated conformation to determine a structural, energetic, thermodynamic or kinetic property of said molecular system.
    • 形成生成的分子系统构象的方法,包括产生所述分子系统的分子动力学轨迹,其中所述轨迹是通过将所述分子系统中的每个原子分配给初始速度矢量和初始构象的一组初始参数来启动的 其中所述分子系统中的每个原子被设置在初始位置,并且其中所述分子动力学轨迹通过计算过程传播,包括:(a)通过计算能量函数的导数来计算施加在每个原子(i)上的电流力 描述所述原子(i)与所述分子中的其它原子之间的相互作用; (b)确定描述沿着所述原子(i)上施加的力的所述轨迹的一部分的平均值的引导力gi; (c)根据方程miai = fi通过调整所述先前位置和速度来确定所述原子(i)的当前位置和速度,其中mi是原子(i)的质量,a i是原子(i)的加速度, 并且fi是通过将在(a)中计算的所述电流力和在(b)中确定的所述引导力相加)而获得的力; (d)用所述原子(i)的当前位置和速度替换所述原子(i)的所述先前位置和速度; (e)重复步骤(a)至(d)以进行一次或多次迭代以产生所述轨迹; 和(f)通过将所述分子的原子设置在给定迭代期间获得的各个当前位置中形成所述产生的构象; 并处理所述产生的构象以确定所述分子系统的结构,能量,热力学或动力学性质。
    • 10. 发明申请
    • SELF-GUIDED MOLECULAR DYNAMICS SIMULATION FOR EFFICIENT CONFORMATIONAL SEARCH
    • 自引导分子动力学模拟有效的一致性搜索
    • WO0010067A9
    • 2001-07-12
    • PCT/US9918302
    • 1999-08-13
    • UNIV GEORGETOWNWU XIONG WUWANG SHAOMENG
    • WU XIONG-WUWANG SHAOMENG
    • G06F17/50G06F19/16G06F19/00
    • G06F19/16
    • A method of forming a generated conformation of a molecular system comprising generating a molecular dynamics trajectory of said molecular system, wherein said trajectory is initiated by assigning to each atom in said molecular system a set of initial parameters comprising an initial velocity vector and an initial conformation wherein each atom in said molecular system is disposed in an initial position, and wherein said molecular dynamics trajectory is propagated by a computational procedure comprising: (a) calculating a current force exerted on each atom (i) by calculating a derivative of an energy function describing interactions between said atom (i) and other atoms in said molecule; (b) determining a guiding force gi describing an average along a portion of said trajectory of a force exerted on said atom (i); (c) determining a current position and velocity of said atom (i) by ajusting said previous position and velocity according to the equation miai = fi, wherein mi is the mass of atom (i), ai is an acceleration of atom (i) and fi is a force obtained by adding said current force calculated in (a) and said guiding force determined in (b); (d) replacing said previous position and velocity of said atom (i) with said current position and velocity of said atom (i); (e) repeating steps (a) to (d) for one or more iterations to generate said trajectory; and (f) forming said generated conformation by disposing the atoms of said molecule in respective current positions obtained during a given iteration; and processing said generated conformation to determine a structural, energetic, thermodynamic or kinetic property of said molecular system.
    • 一种形成生成的分子系统构象的方法,包括产生所述分子系统的分子动力学轨迹,其中所述轨迹是通过将所述分子系统中的每个原子分配给初始速度矢量和初始构象的一组初始参数来启动的 其中所述分子系统中的每个原子被设置在初始位置,并且其中所述分子动力学轨迹通过计算过程传播,包括:(a)通过计算能量函数的导数来计算施加在每个原子(i)上的电流力 描述所述原子(i)与所述分子中的其它原子之间的相互作用; (b)确定描述沿着所述原子(i)上施加的力的所述轨迹的一部分的平均值的引导力gi; (c)通过根据方程miai = fi调整所述先前位置和速度来确定所述原子(i)的当前位置和速度,其中mi是原子(i)的质量,ai是原子(i)的加速度, 并且fi是通过将在(a)中计算的所述电流力和在(b)中确定的所述引导力相加)而获得的力; (d)用所述原子(i)的当前位置和速度替换所述原子(i)的所述先前位置和速度; (e)重复步骤(a)至(d)以进行一次或多次迭代以产生所述轨迹; 和(f)通过将所述分子的原子设置在给定迭代期间获得的各个当前位置中形成所述产生的构象; 并处理所述产生的构象以确定所述分子系统的结构,能量,热力学或动力学性质。