Re: Lennard-Jones potential in coarse grained MD

From: Yongcheng Zhou (
Date: Sun Jan 31 2016 - 00:16:37 CST

Hi Jian and all,

Thanks for your answer to the conversion between standard LJ formula and
the NAMD's LJ formula. What I was really confused is the LJ parameters
provided in the CG parameter file martini-all-nonb.par, for example:

   N0H SC4 -0.83652000 5.27557163

Here I guess eps=-0.836 and Rmin = 5.27 Angstrom. N0H is the backbone of
HIS and SC4 is one of its side chain nodes. The equilibrium distance
between these two CG nodes according to MARTINI force field is 0.32nm.
Thus, extremely large LJ potential and force can be found for these pair
of nodes, indeed much larger than any other type of interactions. I wanted
to know whether I was reading and interpreting these numbers correctly.

Thanks again!


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