[gmx-users] [Fwd: Genbox doubt]

Erik Lindahl lindahl at sbc.su.se
Wed Nov 23 18:27:38 CET 2005


Almost - genbox uses a (usually small) configuration of pre- 
equilibrated solvent. This configuration is repeated to cover your  
system, and then waters outside the box or colliding with the solute  
are removed.

The "spc216.gro" argument is a system of 216 equilibrated SPC waters  
that you can find in share/gromacs/top. It's an ancient system (no  
PME, etc), but good enough for this purpose. However, it is quite  
normal that the solvent/solute will pack a bit better after  
equilibration, so normally the density will be a tad too low - a  
couple of picoseconds of pressure scaling will fix that.



On Nov 23, 2005, at 4:29 PM, Alan Dodd wrote:

> The way I see it, genbox dumps in randomly oriented
> waters until there's no more room, and if the box size
> isn't just right, there's going to be thin gaps near
> the edges where there isn't quite space to fit more
> water in.  The larger the box, the more the rest of
> the box damps this out and hides this effect.  If you
> have NPT conditions (constant pressure) then I think
> it should fix the density as soon as you run any MD,
> but even if you run under constant volume I guess it's
> less than a 1% error... there are bigger things to
> worry about in MD.

Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214

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