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
parameter file; (amber.par)
This is the AMBER96 user defined parameter file for NWChem 3.2 and ARGOS 7.0
Electrostatic 1-4 scaling factor 0.833333
Relative dielectric constant 1.000000
Parameters epsilon R*
Atoms
Ti 47.86700 2.58660E+00 2.20000E-01 1 1111111111
22 1.29330E+00 2.20006E-01 TPS000106 JCP 85, 6720-6727 (1986)
Oi 15.99900 1.41810E+00 3.24500E-01 1 1111111111
8 0.70905E+00 3.24500E-01 TPS000106 JCC 12, 1125-1128 (1991)
Cross
Bonds
Angles
Proper dihedrals
Improper dihedrals
Atom types
Ti 22 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
Oi 8 0 0 0 0 0 0 0 0 0
0 0 0 0 0
0 0 0 0 0
End
sequence file; (TiO2.seq)
1TIO
stop
prepare nw file; (TiO2.nw)
echo
memory noverify heap 1 mb stack 32 mb global 8 mb
start TiO2
prepare
amber
source TiO2.pdb
new_top new_rst
end
task prepare
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