[gmx-users] Energy minimization steps
mark.j.abraham at gmail.com
Wed Dec 21 08:55:01 CET 2016
How many steps does it take you to walk down a mountain to a certain
village? :-) Depends where you are on the mountain, and what's in the way.
But if all you need is to be somewhere near the valley floor to start
equilibration, anything goes!
On Wed, 21 Dec 2016 17:11 Alex <nedomacho at gmail.com> wrote:
> 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
> > Azeem
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