Dear Dr. Vitaly Chaban,
Thanks very much for your patient explanation. Yeah, you are right, that
is what I want to know: how you tuned this parameter?
Since then, if I want to set a new atom type and I know its vdw radius,
so how should I set the sigma for it based on the vdw radius,
which should be in agreement with OPLS-AA/L force filed? Could you give
me some suggestions?
I guess that I have to tune it by myself this time, right? Thanks in
advance!
All the best,
Qinghua Liao
On 04/08/2013 03:21 PM, Dr. Vitaly Chaban wrote:
I think your misunderstanding comes from the belief that sigma (as
they are tabulated in the force field files) should *exactly
correspond* to the VDW diameter, as in encyclopedia.
This is simply not the case. In reality, sigmas in the force fields
are "tuned" in order to give right interatomic distances AFTER you
turn on all the necessary potentials (Coulombic attraction in case of
OPLS).
Dr. Vitaly Chaban
On Mon, Apr 8, 2013 at 3:14 PM, fantasticqhl <fantastic...@gmail.com
<mailto:fantastic...@gmail.com>> wrote:
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!
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
