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> 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>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>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