[gmx-developers] help for integrating minimization algorithm

Wilhelm Bender wilhelm.bender at gmx.de
Sun Dec 4 21:29:59 CET 2016


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

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,


-----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
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