[gmx-users] genbox box size problem

Alexander Björling alex.bjorling at gmail.com
Mon Apr 29 11:30:39 CEST 2013

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

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?

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