[gmx-users] Question about the Marrink's CG model

Li Yang liyang1980_0_0 at 163.com
Wed Sep 9 18:01:44 CEST 2009

Dear GMXers:

I'm sorry to disturb you.

I have a question about the Marrink's coarse-grained model, Marrink, et al. Coarse Grained Model for Semiquantitative Lipid Simulations. J. Phys. Chem. B 2004, 108, 750-760.

In the Marrink's CG model, the electrostatic Coulombic potential is computed via cutoff scheme. In the original paper, the cutoff method is employed "with relative dielectric constant \epsilon=20 for explicit screening". Does it mean the parameter of force field is only customized for the cutoff method? As known that the Ewald method is better than the cutoff scheme for the long-range electrostatic interaction. I want to know whether the Ewald method is also OK for this model? How can I test it? I have simulated a similar system via two method respectively, which includes a big charged nano-scale particle (~6nm). But I find that the results of cutoff scheme are quite different from the PME's results. I don't know which one is right.

Another question is how to get the relative dielectric constant for a CG model. I'm not familiar with this topic, but I think it is the key of the above question perhaps. Yet, there are not some details in the original paper. In some other paper about different CG models, I don't find some information about this topic. Could someone please give me some refs about the computational details?

Thank you very much.

Li Yang

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