abhishek sharma wrote:
sir,
i want to introduce a shell model in ZnS particles and have the
potential data. I gone through your Novel Shell Model for the water
molecule givem in the /share/top as sw.itp.
could you please help me out how I can introduce all these potentials
in my model I have the following data.
Species Charge e
Zn core +2.00
Cd core +2.00
S core +1.03061
S shell −3.03061
C eV/ Å6
Å
Cut-off Å
Buckingham potential A eV
Zn core - S shell 672.288 0.39089
0.0 12.00
Cd core - S shell 1240.9518 0.371852
0.0 12.00
S shell - S shell 1200.0 0.14900
0.0 12.00
k eV/ Å2
Core-shell potential Cut-off Å
S core - S shell 13.302743 0.8
k eV/ rad2
Three-body potential ° 1/ 2
Å Cut-off Å
0
106
S shell - Zn core - S shell 9.42834 109.47
0.3 6.0
107
S shell - Cd core - S shell 3.59468 109.47
0.3 6.0
Torsional potential kt eV m/n rmin
Å rmax Å
Zn core - S shell - Zn core - S shell 0.005 +1 / + 3
2.5 3.0
I would urge you to read chapters 4 and 5 of the manual.
Are these Buckingham potentials for next neighbors as well? Most likely
not, but in that case you need some kind of bond potential.
Anyway, if this system is completely non-bonded then it becomes a bit
more difficult since there are no non-bonded three body interactions
implemented. In that case you need to make a tabulated bonded potential,
for each of the different interactions involved in direct bonds. You can
probably use x2top to generate a topology file for your system, but yu
will have to make your own .n2t input file for it. Check the existing
ffoplsaa.n2t file for reference.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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