then you need to make a new water box, since the
standard one was obtained through simulation with
the normal parameters. leap doesn't place each
water individually, it uses this pre-equilibrated box.
you can make one with waters closer by using different
parameters, but I am not sure if you really want to
do that.
Yam wrote:
> Hi.
>
> What i meant was ... if we want to change the distance between
> molecule and water molecule when we solvate, we will need to put the
> value in "closeness". What about if we want to change the values
> between one water molecule with another water molecule in the waterbox?
>
> thanks.
>
> regards,
> Yam
>
> */"David A. Case" <case.scripps.edu>/* wrote:
>
> On Thu, Dec 15, 2005, Yam wrote:
> >
> > I came across the word "aniso" and "iso" in the solvateoct
> and solvatebox
> > command in the leap program. Anyone know what does that mean?
>
> Please see pp. 71 and 74 of the Users' Manul.
>
> >
> > I'm trying to alter some va! lue for the distance between
> water molecule and
> > water molecule, can anyone please tell me how?
>
> I don't understand the question.
>
> ...dac
>
>
>
>
> __________________________________________________
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Received on Mon Dec 19 2005 - 12:53:01 PST
