[gmx-users] Energy minimization steps
syedazeemullah186 at gmail.com
Wed Dec 21 09:43:15 CET 2016
Thank you Alex and Mark for your replies. :-)
> 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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