[gmx-users] Energy minimization steps

[Alex]

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.


Alex


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