merc mertens wrote:
Dear people,
I am trying to use the MARTINI CG force field from Marrink et al. for a 100
residue protein in water. I use the tools from the Marrink website
(http://md.chem.rug.nl/~marrink/MARTINI/Downloads.html) for preparation of the
necessary gro and itp files. For solvation of my protein I use the water.gro
from the same website. However, using editconf/genbox to do so it is difficult
to judge the density of system. genbox tells me that it is usually around a
value between 220 and 260 g/l depending on boxsize. As the MARTINI forcefield
uses a 1-to-4 mapping I think 250 g/l should correspond to 1000 g/l using an
all-atom representation of my system. Still, I do not know whether these
density values given by genbox are correct. Is there anyway to check this?
Your structure file should have the size of the box recorded - life is
easy if it is cubic. Otherwise, add up your molecules and molar masses
and invoke Avogadro for the mass.
Mark
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