[gmx-users] vdwd option on genbox: Exactly what does it do?

[David Mobley]

David,

Thanks a lot. That helps a whole lot.

(For the list: The reason I needed to do this is that I was getting waters
stuck into my protein when solvating; it would take them forever (well, a
very long time) to escape, and I needed a way to make sure this wouldn't
happen.).

David

On 1/9/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> David Mobley wrote:
> > Dear all,
> >
> > genbox has a -vdwd option which specifies "default vdwaals distance".
> > The documentation isn't too clear about this; does it override what
> > genbox usually uses? Or is it only used for molecules which have no vdW
> > parameters or some such?
> Second.
>
> >
> > For anyone who cares: I'm trying to keep water somewhat further away
> > from the protein when solvating than is typical, and I'm trying to
> > figure out whether using -vdwd is a way to do this, or whether I'll have
> > to make a script to delete all of the waters within my desired cutoff
> > distance from the protein.
> You want to copy the vdwradii.dat file to your working directory and
> edit that.
> >
> > Thanks,
> > David
> >
> >
> > ------------------------------------------------------------------------
> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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