Dear Marat
Thanks a lot. We want to use NWCHEM for classical MD simulation of organic molecules' adsorption from solution on the TiO2 surface. At first we want to be able to use NWCHEM for classical MD simulation. We have removed all the connectivity fields from fragment file. unfortunately we did not find that how add cell size ( Is it necessary, if we do not want to apply periodicity?). Following are used and created files.
Best Regards
Saeed
pdb file;(TiO2.pdb)
ATOM 1 Ti1 TIO 1 5.164 0.702 -0.905
ATOM 2 O1 TIO 1 7.279 0.372 -0.689
ATOM 3 O2 TIO 1 3.184 0.430 -1.379
ATOM 4 Ti2 TIO 1 1.178 0.699 -0.892
ATOM 5 O3 TIO 1 1.158 2.357 0.210
ATOM 6 O4 TIO 1 1.033 1.887 -2.360
ATOM 7 Ti3 TIO 1 1.117 3.460 -1.242
ATOM 8 O5 TIO 1 5.193 2.406 0.075
ATOM 9 O6 TIO 1 5.325 1.847 -2.470
ATOM 10 Ti4 TIO 1 5.242 3.430 -1.446
ATOM 11 O7 TIO 1 3.149 3.820 -1.537
ATOM 12 O8 TIO 1 7.306 3.822 -1.502
END
fragment file;(TIO.frg)
# This is an automatically generated fragment file
- Atom types and connectivity were derived from coordinates
- Atomic partial charges are crude estimates
- 04/30/14 18:11:29
$TIO
12 1 1 0
TIO
1Ti1 Ti 0 0 0 1 1 +2.196000 0.000000
2 O1 Oi 0 0 0 1 1 -1.098000 0.000000
3 O2 Oi 0 0 0 1 1 -1.098000 0.000000
4Ti2 Ti 0 0 0 1 1 +2.196000 0.000000
5 O3 Oi 0 0 0 1 1 -1.098000 0.000000
6 O4 Oi 0 0 0 1 1 -1.098000 0.000000
7Ti3 Ti 0 0 0 1 1 +2.196000 0.000000
8 O5 Oi 0 0 0 1 1 -1.098000 0.000000
9 O6 Oi 0 0 0 1 1 -1.098000 0.000000
10Ti4 Ti 0 0 0 1 1 +2.196000 0.000000
11 O7 Oi 0 0 0 1 1 -1.098000 0.000000
12 O8 Oi 0 0 0 1 1 -1.098000 0.000000
segment file; (TIO.sgm)
- This is an automatically generated segment file
- 04/13/14 13:20:08
4.600000
12 0 0 0 0 0 1 1
0.000000
1Ti1 0 0 0 1 1
Ti 0.000000 0.000000
2 O1 0 0 0 1 1
Oi 0.000000 0.000000
3 O2 0 0 0 1 1
Oi 0.000000 0.000000
4Ti2 0 0 0 1 1
Ti 0.000000 0.000000
5 O3 0 0 0 1 1
Oi 0.000000 0.000000
6 O4 0 0 0 1 1
Oi 0.000000 0.000000
7Ti3 0 0 0 1 1
Ti 0.000000 0.000000
8 O5 0 0 0 1 1
Oi 0.000000 0.000000
9 O6 0 0 0 1 1
Oi 0.000000 0.000000
10Ti4 0 0 0 1 1
Ti 0.000000 0.000000
11 O7 0 0 0 1 1
Oi 0.000000 0.000000
12 O8 0 0 0 1 1
Oi 0.000000 0.000000
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