[gmx-users] Re: genbox box size problem

alex.bjorling alex.bjorling at gmail.com
Mon Apr 29 19:50:56 CEST 2013

Justin Lemkul wrote
> I have seen this exact problem posted before.  The coordinates of the
> water box 
> provided by MARTINI have some coordinate values that basically coincide
> across 
> the periodic box.  With genconf, you can apply the -dist option to space
> them 
> out slightly, then re-equilibrate before using the new configuration as
> input 
> into genbox.

I don't think that's true. Stacking boxes with -nbox 3 3 3 (without -dist)
gives a big box which you can minimize and equilibrate with no trouble. Both
with and without -dist 0.21 0.21 0.21 (0.21 is a suitable MARTINI -vdwd for
genbox), you get big water boxes which behave well. The problems start when
you use them as solvents in genbox.

Xavier's suggestion (stack, minimize, equilibrate, manually cut with a
script) works fine, thanks for the suggestion.

Seems to me there might be a bug in genbox, but I'm not the right person to
make such claims.


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