From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Mon Aug 02 2010 - 03:43:53 CDT
For the protein, using restraints is not a problem.
But for water restraints don't make much sense as one would like to let
water diffuse during equilibration (just keep it away from
the hydrophobic core). The same is true for lipids. They should be free to
move in the xy plane of the membrane, but restrained not to go out of the
plane or turn to much.
My current system is just an alpha helix in the membrane. Probably it would
run OK, even If I just heated it without restraints (but I don't have
enough experience with membrane systems yet to know if this is true or not.
Or if water would penetrate too deep. Maybe if I heat the wrong way I could
introduce some artifacts that would take a long time to relax or something.
This is why I wanted to follow an established membrane equilibration
protocol.
So when equilibrating a membrane system is it really necessary to keep water
out?
Best regards,
Ajasja
On Mon, Aug 2, 2010 at 09:37, Bjoern Olausson <namdlist_at_googlemail.com>wrote:
> On Friday 30 July 2010 16:17:36 Ajasja Ljubetič wrote:
> > Dear NAMD users,
> >
> > does anyone have any experiance using the files generated with CHARMM-GUI
> > membrane builder in NAMD? The xplor psf and the pdb files are of course
> not
> > a problem, but the input files for the equilibration (which consists of 6
> > steps) would need a lot of work to translate to NAMD configurations
> files.
> > Has anybody done this already?
> >
> > For example I know there is the keep_water_out.tcl script (which has been
> > giving me problems during the kcsa tuturial, but I can't remember the
> > details now), but the same could be achieved using tcl boundary forces,
> or
> > the grid forces or perhaps simply by first fixing (or constraining) the
> > water molecules.
> >
> >
> > Best regards,
> > Ajasja
>
> Why not simply use constraints like charmm does and reduce the scaling
> factor.
>
> Something like this:
>
> #Use VMD to set the BETA vaule to the desired constraint
> #(make sure all other BETA values are 0)
> #% set cons [atomselect top "protein"]
> #% $cons set beta 10
> #% set sel [atomselect top all]
> #% $sel writepdb k.pdb
>
> constraints on
> consref k.pdb
> conskfile k.pdb
> conskcol B
> constraintScaling 1.0
> #############################################################
> ## EXECUTION SCRIPT
> ##
> #############################################################
>
> # Minimization
> minimize 20000 ;#
> reinitvels $temp ;#
>
> #500000 = 10ns
> run 20000
> constraintScaling 0.5
> run 20000
> constraintScaling 0.2
> run 20000
> constraintScaling 0.1
> run 20000
> constraintScaling 0.05
> run 20000
> constraintScaling 0
> run 380000
>
> I don't know, if you can switch between the consref/conskfile file in a
> single
> run or if you have to start anoter run if you want to include/exclude other
> Atoms in your consref/conskfile.
>
> Cheers
> Bjoern
>
> --
> Bjoern Olausson
> Martin-Luther-Universität Halle-Wittenberg
> Fachbereich Biochemie/Biotechnologie
> Kurt-Mothes-Str. 3
> 06120 Halle/Saale
>
> Phone: +49-345-55-24942
>
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