Thank you very much.
But if I use smaller values, it cause some problems with the properties of
the system. For instance, I have used RP 2.0 and RW 2.0, could this values
mislead over the values of energy calculated?
Thank you
Lucas
On Tue, Jan 8, 2019 at 12:27 PM David Cerutti <dscerutti.gmail.com> wrote:
> There are defaults for those values. Generally you want RP to not go below
> 2 or 2.5. The solvent:solvent clipping radius can be very high for adding
> small numbers of rare species, so make sure they are spread out. The
> clipping radius is the minimum distance that AddToBox will allow any atoms
> of a new molecule to be placed from existing protein or solvent atoms. The
> "protein" atoms are defined as the first -P atoms of the system, everything
> else is solvent. Add rare, large species of solvent first, then smaller
> and more common ones.
>
> Dave
>
>
> On Tue, Jan 8, 2019 at 9:07 AM David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Tue, Jan 08, 2019, Lucas Bandeira wrote:
> > >
> > >Could one help me with the term "clipping radius". What it exactly means
> > >and how can I find the right values for protein atoms and for solvent
> > atoms
> > >( -RP and -RW in AddToBox).
> >
> > This is not definitive, but I always use RP of 2.5 and RW of 2.8 for
> > either waters or monatomic ions. I remember that years ago I played
> > around with these values (and you can experiment as well), but I don't
> > seem to be able to find the record of how I arrived at these values....
> >
> > If you are adding bigger solvent molecules, you will probably have to
> > experiment some: see the Reference manual for suggestions.
> >
> > [Dave: should we not add some defaults, and suggested values (maybe
> > different than those above) to the Manual?]
> >
> > ....dac
> >
> >
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Received on Tue Jan 08 2019 - 07:00:02 PST
