[gmx-users] Re: genbox box size problem
x.periole at rug.nl
Tue Apr 30 11:43:58 CEST 2013
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
>> the periodic box. With genconf, you can apply the -dist option to space
>> out slightly, then re-equilibrate before using the new configuration as
>> 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.
> View this message in context: http://gromacs.5086.x6.nabble.com/genbox-box-size-problem-tp5007753p5007768.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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