[gmx-users] genbox box size problem

XAvier Periole x.periole at rug.nl
Mon Apr 29 12:22:33 CEST 2013

genbox works best when the box size of the solute is defined as the same as of the water one used to solvate it. So you can build a water box with the dimensions you want and them use it. 

You can build a water box by using genconf -nbox and use a script to cut to the dimensions you need, minimize, equilibrate ... 

Using a bigger box size should work too but it might need to be positioned/centered correctly and the solute too ... 

On Apr 29, 2013, at 11:30, Alexander Björling <alex.bjorling at gmail.com> wrote:

> Dear users,
> I am trying to solvate a MARTINI model, using a pre-equilibrated
> coarse-grained water box. This usually works fine with the following
> command.
> genbox -cs water-1bar-303K.gro -cp 01min.gro -o 02solv -vdwd 0.21
> When I recently increased the box size things started going wrong. As the
> simulation box got bigger than the (-cs) water box, the solvated structure
> ended up containing clear block-shaped regions of higher and lower solvent
> density. I obviously tried stacking the (-cs) box first to make it bigger
> than the box in the (-cp) file,
> genconf -f water-1bar-303K.gro -o water-1bar-303K_big.gro -nbox 3 3 3
> but the problem persisted. Waters actually coincide in the solvated
> structure, so energy minimization is obviously hopeless.
> Is genbox behaving unexpectedly or is this likely an input problem?
> Cheers,
> Alex
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