[gmx-users] Energy minimization steps
nedomacho at gmail.com
Wed Dec 21 07:10:27 CET 2016
This isn't a Gromacs-specific parameter, or, for that matter, anything
that straightforwardly depends on the nature of the system
(solid/fluid/protein/lipid, etc) and its size, aside from maybe trivial
cases. The max number of minimization steps is something that limits an
energy minimization attempt, given the minimization algorithm,
tolerance, the energy step, and, of course, how well-behaved you expect
your system to be. It is a reasonable trial and error guess aimed at
computational efficiency, e.g. not exceeding a certain amount of
computational burden for really bad structures. Alternatively, limiting
the number of minimization steps can help not produce some kind of a
freaky structure when you have several local minima nearby.
On 12/20/2016 10:51 PM, Syed Azeem wrote:
> Hi all,
> What is the basis of inputting the maximum number of energy
> minimization steps in GROMACS?
> Does maximum number of energy minimization steps depend on the number
> of residues?
> I came across many articles wherein the authors have described the
> number of energy minimization steps within which they have minimized
> their protein.
> I have a protein of 596 residues to be simulated.
> Thanks in advance
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