AMBER Archive (2006)

Subject: Re: AMBER: puzzles about solvatoct or solvatebox

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Oct 17 2006 - 11:13:58 CDT

> >> I found that the solute is not in the center of oct-box
> >
> >It sounds like there is a bug in solvateoct.
> >
> Is it really a bug or not? in MD simulations, the solute must be placed
> in the center of the (oct)box? or just being completely buried in the
> solvent is OK? if the latter is YES, then I'll just increase the buffer
> to 12 to completely solvate my system with the cost of more 2400 waters.

The solute could even stick out of the box as long as it can
"fit in" the other side, i.e. if waters have been subtracted
on the other side of the box to allow room for it. Generally
the box periodicity makes up for misplacement in the box.

Bill
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