[gmx-developers] help for integrating minimization algorithm

[Wilhelm Bender]

Hello,

i found an entry point to implement my minimizer. I basically replaced the
search direction inside do_steep() in minimize.c. Now I encounter another
problem: 

as soon as I translate a sequence to a pdb-file I get an alpha-helix as a
start structure. When I minimize by using the integrator "steep" gromacs
seems to penalize anything that wants to break the alpha-helix. I read here
and there that this may be a setting inside gromacs concerning restraints
and constraints. The minimizer that I apply is a (quasi) global optimizer,
therefore I need to be able to find a configuration of my input files for
mdrun such that I can aggressively alter the starting structure without
getting problems with any restraints and constraints ripping apart. 

Do you have a suggestion for a setup in order to do global optimization?

Best Regards and Thank you for any help,

Wilhelm 

-----Ursprüngliche Nachricht-----
Von: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se
[mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] Im Auftrag
von David van der Spoel
Gesendet: Donnerstag, 21. Juli 2016 18:33
An: gromacs.org_gmx-developers at maillist.sys.kth.se
Betreff: Re: [gmx-developers] help for integrating minimization algorithm

On 21/07/16 11:42, Wilhelm Bender wrote:
> Hello,
>
>
>
> Im new to gromacs development therefore I need a few hints about how 
> to extend functionalities concerning the energy minimization. I 
> basically found my entry point for integrating a minimization 
> algorithm that uses a gradient much like do_steep(). Can I somehow 
> take the gradient computed and calculate a norm of it and the add the 
> search direction to the current coordinates? Maybe there is a thread that
I overlooked?
>
>
How about do_cg (conjugate gradients)?

>
> Help would be appreciated J
>
>
>


--
David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec.
Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
--
Gromacs Developers mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developers or
send a mail to gmx-developers-request at gromacs.org.