[gmx-users] Re: genbox box size problem

[XAvier Periole]

We have noticed that g_genbox issue with MARTINI but have not new able to understand where it actually comes from. It might be a bug or just a miss communication of the vdw radius with genbox that appears only with large spheres. 

On Apr 29, 2013, at 19:50, "alex.bjorling" <alex.bjorling at gmail.com> wrote:

> 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.
> 
> Alex
> 
> 
> 
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