[gmx-users] genbox box size problem

Justin Lemkul jalemkul at vt.edu
Mon Apr 29 13:02:35 CEST 2013

On 4/29/13 5:30 AM, Alexander Björling 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?

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.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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