Dear Dr. Vitaly Chaban,
Thanks very much for concern on my research! We are going to the use the
bonded model together with Coulomb and LJ potentials.
My problem is that vdw radius and its sigma do not follow the equation
of Rvdw = pow(2, 1/6)*sigma in the OPLS force field files,
not just for copper. That's why I sent these e-mails for suggestions. I
am sorry for the unclear.
All the best,
Qinghua Liao
On 04/08/2013 01:22 PM, Dr. Vitaly Chaban wrote:
Dear Qinghua Liao -
In that case, I am just wishing you luck with the copper containing
systems.
Are you going to simulate copper-ligand interactions using Coulomb+LJ
potential only? I would guess it is a chemical bonding case. Maybe the
Morse potential (additionally) can be of better service?
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 1:09 PM, fantasticqhl <fantastic...@gmail.com
<mailto:fantastic...@gmail.com>> wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your explanation. I guess that I get what you
mean now! Thanks!
All the best,
Qinghua Liao
On 04/07/2013 11:35 AM, Dr. Vitaly Chaban wrote:
The equation is a direct consequence of LJ-12-6 equation. This
equation is used in OPLS and most other force fields.
The difference you found originate from the fact that, besides LJ
potential, there is much stronger Coulomb potential in the
copper-ion case. If you run simulations, you will see that
copper-ligand distance is smaller than the sum of their sigmas
multiplied by pow (2, 1/6).
Dr. Vitaly Chaban
On Sun, Apr 7, 2013 at 11:28 AM, fantasticqhl
<fantastic...@gmail.com <mailto:fantastic...@gmail.com>> wrote:
Dear Dr. Vitaly Chaban,
Thanks for the explanation. I know this equation. However,
the van der Waals radius and its counterpart sigma in
OPLS-AA/L force field files do not follow this equation.
For example, the vdw radius of copper ion is 1.4 angstrom,
and its sigma is 2.08470e-01 (I guess the unit is nm). pow(2,
1/6) is more than 1, so obviously this equation
does not work with copper. So do other atoms. I guess that
there might be an additional coefficient for this equation in
gromacs. That's the purpose for asking. Thanks very much!
All the best,
Qinghua
On 04/07/2013 10:48 AM, Dr. Vitaly Chaban wrote:
Dear Qinghua -
The formal relation is diameter = pow (2, 1/6) * sigma,
provided that you have only LJ potential in your interacting
subsystem.
If this is not the case, an optimal sigma can only be found
iteratively.
Dr. Vitaly Chaban
On Sun, Apr 7, 2013 at 10:36 AM, fantasticqhl
<fantastic...@gmail.com <mailto:fantastic...@gmail.com>> wrote:
Dear Dr. Vitaly Chaban,
Thanks very much for your reply. My question is the
relationship between van der Waals radius and sigma in
the OPLS-AA/L force filed files of Gromacs.
Of course I did ab initio optimizations of my system,
but I do not know there is some relation between the
optimal bond length (copper--atom of the ligand) and sigma.
Could you please be more clear and give a little
detailed explanation? Thanks very much!
All the best,
Qinghua
On 04/06/2013 06:07 PM, Dr. Vitaly Chaban wrote:
In systems of such kind, everything will depend on
the atom of the ligand,
which coordinated by copper ion.
Perform ab initio geometry optimization and find the
optimal distance. Then
adjust sigma(s).
Dr. Vitaly Chaban
There is a copper ion with four ligands in my
system. I am going to
study this system using MD simulations.
For the vdW parameters, R*=1.74 angstrom and
epsilon=1.14 kcal.mol from
one paper will be used in our
simulations. I already found the parameters of
copper ion (Cu2+) in the
OPLS-AA/L force field files:
sigma= 2.08470e-01, epsilon=4.76976e+00, which
are for Cu2+ without
ligands. The two epsilon are the same,
just with different units.
My question is that I do not know how to convert
the vdW radius to
sigma. I found that the vdw radius of copper is
1.4 angstrom, and the sigma in the force field
file is 2.08470e-01.
Could someone tell me how to do the converting?
Thanks very much!
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