Re: [gmx-users] Energy minimization steps

[Syed Azeem]

Thank you Alex and Mark for your replies. :-)

Azeem

> Hi,
>
> 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!
>
> Mark
>
> On Wed, 21 Dec 2016 17:11 Alex  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.
>>
>>
>> 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
>>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Energy minimization steps

[Mark Abraham]

Hi,

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!

Mark

On Wed, 21 Dec 2016 17:11 Alex  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.
>
>
> 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
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Re: [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


--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

[gmx-users] Energy minimization steps

[Syed Azeem]

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
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.