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.bjorl...@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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