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

[Shuangxing Dai]

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
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