normal Density for octane incorrect even though bonded parameters are correct.

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1 year 11 months ago #8648 by yogi@martini
Hello,

I tried developing martini parameters for Octane. Did atomic simulation to get standard structural data. Only two parameters I had to develop, one bond length and associated bond force constant. So I did it. Got value of 0.455 and 3350 respectively. The bond distribution matched exactly, see here .

However, density and other properties like RDF is not coming out to be correct.
Density (kg/m3) --> NIST value = 688.7, Atomic simulation value = 706, CG simulation value = 995.

RDF is looking like this .

What can be done here?

Thanks
Yogi

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1 year 11 months ago #8649 by riccardo
Hi Yogi,

On a general note, perfectly matching mass densities cannot be expected for Martini. Martini's philosophy is to promote transferability even though this means having, in general, a sub-optimal model for a specific molecule. 
Still, the discrepancy for the mass density of octane you find seems indeed too large, so: how are you computing the density? Just a reminder that the bead masses by default are 72 amu, while CH3-CH2-CH2-CH2 is about 57. If you use gmx density, this will use the mass of the beads found in the itp, which is 72 unless you changed it. This would overestimate the density, and may explain the discrepancy.

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1 year 11 months ago #8650 by yogi@martini
Thanks Riccardo for the reply. On accommodating mass, the density came out to be 788. I think, we cannot expect more than this, error in density ~10%!

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