normal How particle C1 and C2 are different in their interaction.

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2 years 2 months ago #7200 by yogi@martini
Hi,

I got this doubt while reading a Martini paper "Marrink, Siewert J., et al. "The MARTINI force field: coarse grained model for biomolecular simulations." The journal of physical chemistry B 111.27 (2007): 7812-7824. " particle C2 is assigned to be more polar than C1, but where does they account for the polarity in terms of interaction potential, because when I saw martini_v2.1.itp file, LJ interaction parameters are same for C1-C1, C2-C2, and C1-C2 interaction. In fact it is same for other C types. I do see different interaction for C types with P types etc. So if I have simple saturated carbon chain, will it matter which C type I take? if yes how?
Please help.

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2 years 2 months ago - 2 years 2 months ago #7201 by riccardo
The self-interaction level is indeed the same for C1 and C2, as well as the C1-C2 interaction. So, if in your simulation box you have a mixture of the two, you are actually simulating all equal particles. However, as you noted, the fact that they interact differently with, for example, W (particle P4), will give rise to a different partitioning (see table 3 of SJ Marrink et al. 2007 JPhysChemB, HD/W partitioning, for example): namely, C2 particles will interact more favourably with water (P4 particles), hence they are more polar.
Last edit: 2 years 2 months ago by riccardo.

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