Thanks for the fast reply,
I think the easiest for us would be build something similar to the WATBOX216
model but with our solvent molecules instead of water.
We are using methane molecules to simulate an hydrophobic environment,
so we run simulations at constant volume, and we need to have the starting
density properly defined.
I've read that WATBOX216 was equilibrated through Monte-Carlo simulations, but
does anybody know why it contains 216 molecules, and not 125, or 343 or 512?
I mean, any idea about the importance of the size of this model box?
Thanks again,
xavi
________________________________________________________
Xavier Deupi
Computational Medicine Lab
Biostatistics Unit. School of Medicine
Universitat Autonoma de Barcelona. CATALUNYA (Spain)
Phone : (3493)-581.38.12
E-mail: Xavier.Deupi_at_uab.es
________________________________________________________
-
> On Wed, Jul 17, 2002, Xavier Deupi wrote:
> >
> > In the "old" edit program, you could build general solvent boxes using the
> > GEN control word.
> > Within this option you were able to set the starting density of your box
> > with the keyword SCALE.
> >
> > a) Is there any way to do that with the leap SolvateBox option?
>
> No. Suggested patches are welcome. I think the view of the current
> developers is that the poor intial density is not a serious problem: it
> can be removed with a fairly short constant pressure equilibration (which is
> needed anyway for other purposes). But we are certainly willing to consider
> good ideas for getting a better initial set of coordinates.
Received on Thu Jul 18 2002 - 16:16:17 PDT
