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Code 13: topol.top (ASCII file)
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# define _FF_OPLS
# define _FF_OPLSAA
[ defaults ]
; nbfunc comb - rule gen - pairs fudgeLJ fudgeQQ
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yes
0.5 0.5
;;; LOAD ATOM TYPES
# include " path / top / EMI_AtTy_lopes . itp "
# include " path / top / BMI_AtTy_lopes . itp "
# include " path / top / OMI_AtTy_lopes . itp "
# include " path / top / Cl_AtTy . itp "
# include " path / top / BF4_AtTy . itp "
# include " path / top / TFSI_AtTy_lopes . itp "
;;; LOAD OPLS FF
# include " localgromacspath / share / gromacs / top / oplsaa . ff /
ffnonbonded . itp "
# include " localgromacspath / share / gromacs / top / oplsaa . ff / ffbonded .
itp "
;;; LOAD MOLECULES *. itp
# include " path / top / EMI_lopes . itp "
# include " path / top / BMI_lopes . itp "
# include " path / top / OMI_lopes . itp "
# include " path / top / Cl . itp "
# include " path / top / BF4 . itp "
# include " path / top / TFSI_lopes . itp "
[ system ]
; Name
Neat BMI BF4
[ molecules ]
BMI 200
BF4 200
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Charges
In the case of organic molecules the OPLS-AA forcefield has proved to give reasonable results
in many cases. But it might be a good idea to play with the charges. With Gaussian03 [3]
charges can be calculated based on quantum mechanics. An input file .com for calculating
charges of a molecule would look like
Code 14: Head of Gaussian input .com (ASCII file)
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% Nprocshared =4
% Mem =1 GB
% Chk = scna_HF_6 -31 Gd . chk
# p hf /6 -31 g ( d ) nosymm geom = connectivity pop = chelpg
with the addition of particle positions and bond information.
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