[gmx-users] Reading Force field

[Ben Tam]

Dear Gromacs User,


I am trying to do a bit of debugging on the force field, how can I read the individual interaction between non-bonded potential? If it is not possible, can anyone tell me this is around the correct range for the lennard jones potential?  I am trying to debugging because when I am doing classical binding energy calculation, it gives me -4000 kJ/mol force (which is very unrealistic).


[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.833

[ atomtypes ]
; name      at.num  mass     charge ptype  sigma      epsilon
Mg   12     24.3050    1.567       A       0.2691      0.464395
C1    6     12.0107    0.937       A   3.39967e-01  3.59824e-01  ;AMBER
C2    6     12.0107   -0.326       A   3.39967e-01  3.59824e-01  ;AMBER
C3    6     12.0107    0.458       A   3.39967e-01  3.59824e-01  ;AMBER
C4    6     12.0107   -0.235       A   3.39967e-01  3.59824e-01  ;AMBER
O1    8     15.9994   -0.914       A   2.95992e-01  8.78640e-01  ;AMBER
O2    8     15.9994   -0.767       A   2.95992e-01  8.78640e-01  ;AMBER
O3    8     15.9994   -0.907       A   2.95992e-01  8.78640e-01  ;AMBER
H4    1     1.00794    0.191       A   2.59964e-01  6.27600e-02  ;AMBER
;
C5    6     12.0107    0.795       A   3.39967e-01  3.59824e-01  ;AMBER
C6    6     12.0107   -0.090       A   3.39967e-01  3.59824e-01  ;AMBER
C7    6     12.0107   -0.164       A   3.39967e-01  3.59824e-01  ;AMBER
C8    6     12.0107    0.119       A   3.39967e-01  3.59824e-01  ;AMBER
C9    6     12.0107    0.005       A   3.39967e-01  3.59824e-01  ;AMBER
C10   6     12.0107   -0.032       A   3.39967e-01  3.59824e-01  ;AMBER
C11   6     12.0107   -0.174       A   3.39967e-01  3.59824e-01  ;AMBER
C12   6     12.0107   -0.269       A   3.39967e-01  3.59824e-01  ;AMBER
C13   6     12.0107    0.632       A   3.39967e-01  3.59824e-01  ;AMBER
O4    8     15.9994   -0.607       A   2.95992e-01  8.78640e-01  ;AMBER
O5    8     15.9994   -0.517       A   2.95992e-01  8.78640e-01  ;AMBER
HO    1     1.00794    0.340       A       0.0000      0.000000  ;AMBER
H7    1     1.00794    0.131       A   2.59964e-01  6.27600e-02  ;AMBER
H12   1     1.00794    0.106       A   2.64953e-01  6.56888e-02  ;AMBER
F     9     18.9984   -0.203       A   3.11815e-01  2.55224e-01  ;AMBER
HW    1     1.00794    0.417       A   3.06647e-01  8.80314e-01
OW    1     15.9994   -0.834       A   3.15061e-01  6.36386e-01

Thank you very much.

Best regards,

Ben