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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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