<div dir="ltr">Hi,<br><br><div class="gmail_quote"><div dir="ltr">On Mon, Dec 5, 2016 at 7:30 AM Wilhelm Bender <<a href="mailto:wilhelm.bender@gmx.de">wilhelm.bender@gmx.de</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br class="gmail_msg">
<br class="gmail_msg">
i found an entry point to implement my minimizer. I basically replaced the<br class="gmail_msg">
search direction inside do_steep() in minimize.c. Now I encounter another<br class="gmail_msg">
problem:<br class="gmail_msg">
<br class="gmail_msg">
as soon as I translate a sequence to a pdb-file I get an alpha-helix as a<br class="gmail_msg">
start structure. When I minimize by using the integrator "steep" gromacs<br class="gmail_msg">
seems to penalize anything that wants to break the alpha-helix.</blockquote><div><br></div><div>Sure. Those hydrogen bonds make for a pretty steep-walled energy minimum, and usually the minimizer's job is to follow the gradient.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> I read here<br class="gmail_msg">
and there that this may be a setting inside gromacs concerning restraints<br class="gmail_msg">
and constraints. The minimizer that I apply is a (quasi) global optimizer,<br class="gmail_msg">
therefore I need to be able to find a configuration of my input files for<br class="gmail_msg">
mdrun such that I can aggressively alter the starting structure without<br class="gmail_msg">
getting problems with any restraints and constraints ripping apart.<br class="gmail_msg">
<br class="gmail_msg">
Do you have a suggestion for a setup in order to do global optimization?<br class="gmail_msg"></blockquote><div><br></div><div>Well, you could avoid using constraints, and fail to add any restraints, and otherwise choose emstep to be small.</div><div><br></div><div>I presume you are operating in implicit/no solvent in order that you can get anything done - there's a reason why good MC move sets for compact condensed-phase models are elusive.</div><div><br></div><div>Mark</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Best Regards and Thank you for any help,<br class="gmail_msg">
<br class="gmail_msg">
Wilhelm<br class="gmail_msg">
<br class="gmail_msg">
-----Ursprüngliche Nachricht-----<br class="gmail_msg">
Von: <a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" class="gmail_msg" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a><br class="gmail_msg">
[mailto:<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se" class="gmail_msg" target="_blank">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] Im Auftrag<br class="gmail_msg">
von David van der Spoel<br class="gmail_msg">
Gesendet: Donnerstag, 21. Juli 2016 18:33<br class="gmail_msg">
An: <a href="mailto:gromacs.org_gmx-developers@maillist.sys.kth.se" class="gmail_msg" target="_blank">gromacs.org_gmx-developers@maillist.sys.kth.se</a><br class="gmail_msg">
Betreff: Re: [gmx-developers] help for integrating minimization algorithm<br class="gmail_msg">
<br class="gmail_msg">
On 21/07/16 11:42, Wilhelm Bender wrote:<br class="gmail_msg">
> Hello,<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
> Im new to gromacs development therefore I need a few hints about how<br class="gmail_msg">
> to extend functionalities concerning the energy minimization. I<br class="gmail_msg">
> basically found my entry point for integrating a minimization<br class="gmail_msg">
> algorithm that uses a gradient much like do_steep(). Can I somehow<br class="gmail_msg">
> take the gradient computed and calculate a norm of it and the add the<br class="gmail_msg">
> search direction to the current coordinates? Maybe there is a thread that<br class="gmail_msg">
I overlooked?<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
How about do_cg (conjugate gradients)?<br class="gmail_msg">
<br class="gmail_msg">
><br class="gmail_msg">
> Help would be appreciated J<br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
><br class="gmail_msg">
<br class="gmail_msg">
<br class="gmail_msg">
--<br class="gmail_msg">
David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec.<br class="gmail_msg">
Biol., Uppsala University.<br class="gmail_msg">
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:018-471%2042%2005" value="+46184714205" class="gmail_msg" target="_blank">+46184714205</a>.<br class="gmail_msg">
<a href="mailto:spoel@xray.bmc.uu.se" class="gmail_msg" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" rel="noreferrer" class="gmail_msg" target="_blank">http://folding.bmc.uu.se</a><br class="gmail_msg">
--<br class="gmail_msg">
Gromacs Developers mailing list<br class="gmail_msg">
<br class="gmail_msg">
* Please search the archive at<br class="gmail_msg">
<a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" rel="noreferrer" class="gmail_msg" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before<br class="gmail_msg">
posting!<br class="gmail_msg">
<br class="gmail_msg">
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="noreferrer" class="gmail_msg" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br class="gmail_msg">
<br class="gmail_msg">
* For (un)subscribe requests visit<br class="gmail_msg">
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" rel="noreferrer" class="gmail_msg" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or<br class="gmail_msg">
send a mail to <a href="mailto:gmx-developers-request@gromacs.org" class="gmail_msg" target="_blank">gmx-developers-request@gromacs.org</a>.<br class="gmail_msg">
<br class="gmail_msg">
--<br class="gmail_msg">
Gromacs Developers mailing list<br class="gmail_msg">
<br class="gmail_msg">
* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" rel="noreferrer" class="gmail_msg" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br class="gmail_msg">
<br class="gmail_msg">
* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" rel="noreferrer" class="gmail_msg" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br class="gmail_msg">
<br class="gmail_msg">
* For (un)subscribe requests visit<br class="gmail_msg">
<a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" rel="noreferrer" class="gmail_msg" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org" class="gmail_msg" target="_blank">gmx-developers-request@gromacs.org</a>.<br class="gmail_msg">
</blockquote></div></div>