[gmx-users] relaxing proteins gradually - how to set constraints?

[Justin A. Lemkul]

Quoting Sebastian Kruggel <kruggel at chemie.uni-hamburg.de>:

> Dear gmx-users,
>
>
>
> I want to relax some protein structures *gradually* using steepest descent,
> first fixing everything but the hydrogens, than tethering just the backbone
> and finally in a third step do the minimization of the complete structure.
>
> In the manual / mdp-options I can only find the opposite:
>
> > hbonds
>
> > Convert the bonds with H-atoms to constraints.
>
>
>
> I chose oplsaa-forcefield (because want to take into account druglike
> molecules).
>
> Is there another way than the mdp-file to put these constraints or do I miss
> anything in general?

I think what you are looking for are position *restraints*, not bond
constraints.

http://wiki.gromacs.org/index.php/position_restraints

-Justin

>
> Thanks in advance
>
>
>
> Sebastian
>
>
>
>
>
> --
>
>
>
> Sebastian Kruggel
>
> Institut für Pharmazie
>
> Raum 112
> Bundesstr.45
> D 20146 Hamburg
>
> Tel. +49(0)40 42838 3626
>
>
>
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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