[gmx-users] density and CG MARTINI force field
Mark.Abraham at anu.edu.au
Tue Apr 15 16:47:32 CEST 2008
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.
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