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

[Bjoern Windshuegel]

Hi,

try to use freeze groups (p. 15 in the manual) in combination with an index 
file.

Best regards,

Björn



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

-- 
Dr. Björn Windshügel

Department of Pharmaceutical Chemistry
University of Kuopio
P.O. Box 1627
70211 Kuopio, FINLAND

Email: bjorn.windshugel at uku.fi
Phone: (+358) 17 162463
Fax:   (+358) 17 162456
Web:   www.uku.fi/farmasia/fake/modelling/index.shtml