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On 19/07/11, "Marzinek, Jan" <j.marzine...@imperial.ac.uk> wrote:
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> On 19/07/11, "Marzinek, Jan" <j.marzine...@imperial.ac.uk> wrote:
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> Dear Gromacs Users,
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> As I know for the Energy Minimization algorithms both Steepest Descent and
> Conjugate Gradient will not provide a global minimum of the potential energy
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> Does anyone know how Gromacs choose the starting point on the potential
> energy hypersurface for the beginning of Energy Minimization?
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> You choose it with the starting configuration you provide to grompp.
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> Mark
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> Hi,
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> Thank you for your response. I understand that you start from the coordinates
> which you specify in your gro file -> Input. But where Gromacs start on the
> potential energy
> surface as it has many local minima, maxima, saddle points.
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GROMACS starts with the configuration you provide.
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> Will it always go to the closest local minimum which is not global minimum?
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Various optimization algorithms can be chosen in the .mdp file. Those
algorithms are deterministic, but their properties vary. They will find a
nearby local minimum eventually, but not necessarily the same one, or in a
given number of steps. See manual or
http://en.wikipedia.org/wiki/Energy_minimization
Mark
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--
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