AMBER Archive (2002)

Subject: Re: correction about solvateOct

From: Michael Jakusch (michael.jakusch_at_pharma.anbi.ethz.ch)
Date: Fri Jul 19 2002 - 04:49:48 CDT

On Fri, Jul 19, 2002 at 11:09:58AM +0200, Nikolai Smolin wrote:
> I did not understand what means 'iso' option in this command.
> If I want to use in my simulation PME is it necessary to use
> this option for preparation my box or not?
> I tried with this option and without . And I recieved different number
> atoms in my system:
>
> alignAxes protein
> solvateOct protein WATBOX216 12,0 iso 0,75 in this case 28223 atoms
> in box
>
> alignAxes protein
> solvateOct protein WATBOX216 12,0 0,75 in this case 19748 atoms in box
>
> What I made wrong?
> Or it is correct?

It is correct - as far as I understood "iso" means that you get "a
cube with the corners chopped off" instead of (smaller) "cuboid with
the corners ...". Hence the larger number of waters added.

> What way for preparation box with less number of particles perfect?

You definitely have to use the "iso" option!!!
Otherwise sander will not understand the oct. box correctly and will
treat it as rectangular with the same dimensions (i.e. only
half-filled with water, density ~ 0.5). At least, this was what
experienced ...

HTH

Michael 

-- 
Dr. Michael Jakusch

ETH - Swiss Federal Institute of Technology
Department of Applied Biosciences
Winterthurerstrasse 190
CH-8057 Zürich
Switzerland
Phone: +41.1.635 60 71
Fax:   +41.1.635 68 84
email: michael.jakusch_at_pharma.anbi.ethz.ch