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
