Re: Lennard-Jones potential in coarse grained MD

Date: Sat Jan 30 2016 - 01:19:17 CST

dear Yongcheng,
for standard form,
  Vf = 4 * eps * ( (sig/r)^12 - (sig/r)^6 )

if you set
  sig = Rmin / sqrt[6]{2} = Rmin / exp(ln(2)/6),

you will got the NAMD form,
  Vn = eps * ( (Rmin/r)^12 - 2*(Rmin/r)^6 )

Jian Liu
From: Yongcheng Zhou
Date: 2016-01-30 14:36
To: namd-l
Subject: namd-l: Lennard-Jones potential in coarse grained MD
Hi there,
I am running residue-based coarse grained MD using NAMD, but was a bit
confused by the formula of the Lennard-Jones potential used in this type
of coarse grained simulation. The two major papers on the MARTINI force
field both said that the Lennard-Jones potential is given by the standard
12-6 form, V = 4 * ep * ( (sig/r)^12 - (sig/r)^6 ). This form is different
from the that in the full atomic NAMD parameter file in the
par_all27_prot_lipid.inp, where v = eps ( (sig/r)^12 - 2 (sig/r)^6 ), with
a coefficient 2 in front of the 6-term. The coarse grained parameter file
in NAMD does not give a formula for LJ potential, although I guess it
follows the same as in the all atomic parameter file.
I would appreciate if anyone can help clarify the coarse grained LJ
potential formula along with the parameter file.

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