[gmx-users] combination rules -- the part about the combinationrules

[Shuangxing Dai]

Thanks for your answer. I changed the non-bond parameters in ffgmxnb.itp.  like
; i    j   func     a        b    c6
Zn  O        2     ...     .....   .... 
But error occured..
 

ERROR 1 [file ffgmxnb.itp, line 270]:

  Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)





ERROR 2 [file ffgmxnb.itp, line 271]:

  Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)





ERROR 3 [file ffgmxnb.itp, line 272]:

  Trying to add Buck.ham (SR) while the default nonbond type is LJ (SR)



I think I have indicated that the function type is 2 (means Buckingham). Anything else need to do with this ?

Also, I want to fix some atoms in the boundary and specify displacement to some atoms, anayone knows how to do this? 

Thank you in advance.

  ----- Original Message ----- 
  From: Berk Hess 
  To: Discussion list for GROMACS users 
  Sent: Wednesday, February 18, 2009 11:39 AM
  Subject: RE: [gmx-users] combination rules -- the part about the combinationrules


  Hi,

  No pairtypes are for bonded pair interactions,
  not for combinations of non-bonded interactions.

  The manual tells you how to do this:
  [ nonbond_params ]
  A_ii A_jj  2  a  b  c6

  Berk

  > Date: Wed, 18 Feb 2009 13:31:43 -0500
  > From: chris.neale at utoronto.ca
  > To: gmx-users at gromacs.org
  > Subject: [gmx-users] combination rules -- the part about the combination rules
  > 
  > For LJ interactions, use [ pairtypes ]. For Coulombics there is 
  > unfortunately no analogous solution. I am not clear about exactly what 
  > you want to do. What "parameters" are you interested in, or by this do 
  > you just mean LJ and Q?
  > 
  > Chris.
  > 
  > -- original message --
  > 
  > Hello,
  > I was wondering how to set up parameters for interactions between 
  > two different atoms A and B. Since for Gromacs parameters are defined 
  > to each kind of atom, I cannot specify parameters between A and B. For 
  > Buckingham potential, the rule was:
  > A_ij=(A_ii * A_jj)^(1/2)
  > So anyone know how to specify this value while not using the 
  > combination rules?
  > --snip--
  > 
  > 
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