[gmx-users] How to use Buckingham potentials ?

[Mark Abraham]

On 15/02/2012 5:42 PM, ramesh cheerla wrote:
> Dear Gromacs users,
>
>                                I am planing  to use buckingham 
> potential for the non-bonded interactions  of my system. I know that 
> by changing the nbfunc to 2 in [ defaults ] directive of topology will 
> allow to use the Buckingham potential , But I don't know how to 
> specify the  A, B,C values in the ffnonbonded.itp file.

With [ nonbond_params], not [atomtypes] or [pairtypes]. See table 5.4 of 
section 5.7.1 of manual.

Mark

>  what values should I specify in the  [ atomtypes ]  directive . As i 
> know  only A,B,C values for the pairs of atoms  so i have tried by  
> specifying  A,B,C values both in  [ atomtypes ] and  [ pairtypes ] as
>
> [ atomtypes ]
> ;name   at.num     mass          charge    ptype        
> A                      B                      C
> CC32A      6       12.01100        0.1030    A       132277.5784    
> 33.05785124    0.002710395
> HCA2       1       1.00800         0.0355      A       29962.4608     
> 41.58004158    0.000212547
> OC30A      8       15.999400      -0.3480   A       243922.5976    
> 40.2414486921  0.000803746
> [ pairtypes ]
> ; i               j       func       A                         
> B                        C
> OC30A   OC30A   2       243922.5976    40.2414486921  0.000803746
> OC30A   CC32A   2       179625.8144    36.297640653   0.001476115
> OC30A   HCA2    2       85489.9984     40.899795501   0.000413379
> CC32A   CC32A   2       132277.5784    33.05785124    0.002710395
> CC32A   HCA2    2       62955.3928     36.832412523   0.000759396
> HCA2    HCA2    2       29962.4608     41.58004158    0.000212547
> ;########### I have given the A(in KJ/mol), B(in nm^-1), C(in Kj/mol*nm^6)
> ;D = A, B = 1/P, C = E
>
>
> Doing so , grompp is showing the following errors
>
>    ERROR 5 [file ffnonbondedpeo.itp, line 13]:
>   Too many parameters or not enough parameters for topology B
>
>
> ERROR 6 [file ffnonbondedpeo.itp, line 14]:
>   Too many parameters or not enough parameters for topology B
>
> Generated 6 of the 6 non-bonded parameter combinations
> Excluding 3 bonded neighbours molecule type 'polymer'
>
> ERROR 7 [file topol.top, line 1652]:
>   ERROR: The cut-off length is longer than half the shortest box vector or
>   longer than the smallest box diagonal element. Increase the box size or
>   decrease rlist.
> ------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: grompp.c, line: 1372
>
> Fatal error:
> There were 7 errors in input file
> -------------------------------------------------------
>
>
> Any help will be highly appreciated.
>
>
> Regards,
> Ramesh Cheerla
>
>

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