[gmx-users] nonbonded LJ parameters

Nuno R. L. Ferreira nunolf at ci.uc.pt
Wed Jan 19 12:39:50 CET 2005

  ----- Original Message ----- 
  From: Sabrina Costa 
  To: gmx-users at gromacs.org 
  Sent: Wednesday, January 19, 2005 11:29 AM
  Subject: [gmx-users] nonbonded LJ parameters

  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 ?

  Hi Sabrina

  The Gromos van der walls parameters for an atom pair I,J are derived from the relations stated by you.

  But, and there's always a but, since gromos f.fs does not contain a special term in the interaction function in order to mimic hydrogen bonding properties of polar atoms, their C12 (polar atoms) van der waals has been increased. I'm quoting part of gromos manual.  

  So, when dealing with polar atoms, the C12 is higher than the one defined in [pairtypes] field.



   Waiting for your reply, thanks a lot



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