[gmx-users] combination rules -- the part aboutthecombinationrules

[Shuangxing Dai]

No. I only changed 3 lines in ffgmxnb.itp. But there are hundreds of lines of error informaion like this:
ERROR 77 [file ffgmxnb.itp, line 144]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 78 [file ffgmxnb.itp, line 145]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 79 [file ffgmxnb.itp, line 146]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 80 [file ffgmxnb.itp, line 147]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 81 [file ffgmxnb.itp, line 148]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 82 [file ffgmxnb.itp, line 149]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 83 [file ffgmxnb.itp, line 150]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 84 [file ffgmxnb.itp, line 151]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)


ERROR 85 [file ffgmxnb.itp, line 152]:
  Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)

  ----- Original Message ----- 
  From: Berk Hess 
  To: Discussion list for GROMACS users 
  Sent: Sunday, February 22, 2009 3:03 PM
  Subject: RE: [gmx-users] combination rules -- the part aboutthecombinationrules


  Hi,

  Is line 68 one of the lines you have added, or another one?

  Berk

  > From: shuangxingdai at gmail.com
  > To: gmx-users at gromacs.org
  > Subject: Re: [gmx-users] combination rules -- the part aboutthe combinationrules
  > Date: Sun, 22 Feb 2009 14:55:21 -0700
  > 
  > Thank you. I have referred to the manual and changed these parts as the 
  > manual told me:
  > in ffgmx.itp:
  > [ defaults ]
  > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
  > 2 1 no 1.0 1.0
  > 
  > in ffgmxnb.itp:
  > [ nonbond_params ]
  > ; i j func a b c6
  > O O 2 92137.86 45.62876437 3090
  > ZN O 2 51108.27 27.92516056 0
  > ZN ZN 2 0 0.1 0
  > But there is no change in the generated .top file.
  > When I use grompp, the errors are :
  > ERROR 1 [file ffgmxnb.itp, line 68]:
  > Trying to add LJ (SR) while the default nonbond type is Buck.ham (SR)
  > Maybe somewhere else need to be changed. Anyone knows why and how?
  > Thank you in advance.
  > 
  > ----- Original Message ----- 
  > From: "Mark Abraham" <Mark.Abraham at anu.edu.au>
  > To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
  > Sent: Friday, February 20, 2009 6:02 PM
  > Subject: Re: [gmx-users] combination rules -- the part aboutthe 
  > combinationrules
  > 
  > 
  > > Shuangxing Dai wrote:
  > >> 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 ?
  > >
  > > ... specify that the default nonbonded type is not LJ? Have a look in 
  > > Chapter 5 of the manual.
  > >
  > >> Also, I want to fix some atoms in the boundary and specify displacement 
  > >> to some atoms, anayone knows how to do this?
  > >
  > > You can freeze groups of atoms, or use position restraints, or pull groups 
  > > of atoms, but you should look first in the manual for the information that 
  > > is there.
  > >
  > > Mark
  > > _______________________________________________
  > > gmx-users mailing list gmx-users at gromacs.org
  > > http://www.gromacs.org/mailman/listinfo/gmx-users
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  > 
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