Re: keeping a protein in a solvation box

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 12 2012 - 18:50:17 CDT

Thanks Aaron! You beat me to this.

However, I can see another email coming requesting to clarify, so I'm
pasting here the example configuration. The last time I sent this to
namd-l was a while ago and may not show up easily in a keyword search.

colvar {

    name com
    width 1.0

    distance {
        group1 {
            # write your atom selection as per the user's manual
        }
        group2 {
            # change the position of this dummyAtom if you want a different
            # point as the center
            dummyAtom (0.0, 0.0, 0.0)
        }
    }
}

colvar {

    name orient
    width 0.05

    orientation {
        atoms {
            # write your atom selection as per the user's manual
        }
        refPositionsFile reference_coordinates.pdb
    }
}

harmonic {
    colvars com orient
    forceConstant 10.0
    centers 0.0 (1.0, 0.0, 0.0, 0.0)
}

On Tue, Jun 12, 2012 at 7:45 PM, Aaron Oakley <aarono_at_uow.edu.au> wrote:

> You could use collective variables to remove the rotation/translation
> component of your macromolecule.
>
> a++
>
> On 13/06/2012, at 8:44 AM, Dr. Eddie wrote:
>
> > Hi all,
> > What is the best way to keep a protein inside a solvation box?
> >
> > With wrapwater and wrapall on my protein still climbs out of the box
> (presumably still experiencing solvation due to periodic boundary
> conditions, but I can't be sure). I'd like the protein to stay in the box.
> Should I fix one single atom in the protein? Is there a better way than
> just making an enormous box?
> > Thanks,
> > Eddie
> >
>
>
>
>

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