[gmx-users] nonbonded LJ parameters

Sabrina Costa sabroggio at yahoo.com.br
Wed Jan 19 12:29:19 CET 2005

Hy all, 

I trying to understand differences between two parametrization for the LJ parameters for the Fluor atom looking for the equilibrium distance and the energy at this point, using some atoms of interest in the system TFE-Water. 

I try to reproduce the parameters in ffG43a1nb.itp using the geometrical approach  C12(i,j)=sqrt(C12(i,i)*C12(j,j). My surprise is that in the atom list we have:

[ atomtypes ]
;name        mass      charge   ptype            c6           c12
    O     0.000      0.000     A  0.0022619536  7.4149321e-07
  OA     0.000      0.000     A  0.0022619536  1.505529e-06

  OW     0.000      0.000     A  0.0026173456  2.634129e-06
    N     0.000      0.000     A  0.0024364096  1.692601e-06
    F     0.000      0.000     A  0.0011778624  7.6073284e-07


[ nonbond_params ]
; i    j func          c6           c12                                c12=sqrt(c12(i)*c12(j)
      OA        O  1  0.0022619536  1.380375e-06             1.0565697e-06
      OA       OM  1  0.0022619536  2.258907e-06           
      OW        O  1  0.0024331696  1.825875e-06            1.3975653e-06
      OW       OM  1  0.0024331696  2.987943e-06          
      OW       OA  1  0.0024331696  1.991421e-06          1.991421e-06 - !!!!!!!!
       N        O  1  0.0023475616  2.185875e-06              1.1202911e-06
       N       OM  1  0.0023475616  3.577063e-06            
       N       OA  1  0.0023475616  2.384061e-06             1.596327e-06
       N       OW  1  0.0025252576  3.153489e-06            2.111523e-06
       F        O  1  0.0016322592  7.5105142e-07            7.5105142e-07  !!!!!!
       F       OM  1  0.0016322592  7.5105142e-07          
       F       OA  1  0.0016322592  1.505529e-06            1.0701894e-06
       F       OW  1  0.0017558112  1.991421e-06           1.4155806e-06      
       F        N  1  0.0016940352  2.384061e-06              1.1347322e-06

As you can see some values follows the rule others no. The question is? Am I wrong in use the rule to obtain the combinations for different atoms i and j ? In this case how can I obtain these values ? By the other hand, if this is not the case, what is wrong ?

 Waiting for your reply, thanks a lot



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