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

[Sebastian Kruggel]

Hi Bjoern

thanks a lot, for the hint, I tried to freeze the (default-)group Protein-H
and also a CL- I had to add before with genion, so my em.mdp looks like

...
freezegrps     = Protein-H CL-
freezedim      = Y Y Y Y Y Y
...

I just wonder why grompp says

...
Freeze       has 3 element(s): Protein-H CL- rest
...

Because that way there isn't much left to minimize ?!

Best regards
Sebastian

--
 
Sebastian Kruggel
Institut für Pharmazie
Raum 112 
Bundesstr.45 
D 20146 Hamburg
Tel. +49(0)40 42838 3626
 
> -----Ursprüngliche Nachricht-----
> Von: Bjoern Windshuegel [mailto:bjorn.windshugel at uku.fi]
> Gesendet: Montag, 2. Juni 2008 13:36
> An: gmx-users at gromacs.org
> Cc: Sebastian Kruggel
> Betreff: Re: [gmx-users] relaxing proteins gradually - how to set
> constraints?
> 
> 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