[gmx-developers] help for integrating minimization algorithm

[David van der Spoel]

On 04/12/16 21:29, Wilhelm Bender wrote:
> 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?
Use a program to generate random starting structures or generate 
structures by running an MD simulation at high temperature.


>
> 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
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-- 
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