[gmx-users] Buckingham potential

[Stefano Piana]

David wrote:


> check your tpr file. the parameters may be nonsensical. if you specifiy
> reasonable values under
> [ nonbond_params ]
> 
> it should work. please note the units should be nm and kJ/mol

HI David,
thanks for your answer, of course as a first attempt I generated a force field 
file with more reasonable values, here it is:

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
      2       1        yes      0.0     0.0

[ atomtypes ]
C         1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
O         1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
Mg        1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00
Ox        1.00000       0.000       A 0.00000E+00 0.00000E+00 0.00000E+00

[ nonbond_params ]
C    C         2   0.000000E+00   0.000000E+00   0.000000E+00
C    O         2   0.000000E+00   0.000000E+00   0.000000E+00
C    Mg        2   0.115780E+11   0.833333E+02   0.000000E+00
C    Ox        2   0.192964E+07   0.509341E+02   0.000000E+00
O    O         2   0.388856E+06   0.407337E+02   0.000000E+00
O    Mg        2   0.000000E+00   0.000000E+00   0.000000E+00
O    Ox        2   0.000000E+00   0.000000E+00   0.000000E+00
Mg   Mg        2   0.000000E+00   0.000000E+00   0.000000E+00
Mg   Ox        2   0.661633E+05   0.321054E+02   0.000000E+00
Ox   Ox        2   0.659658E+07   0.509965E+02   0.210455E-02


The energy is always "nan", regardless of the values that you can put in your 
buck potentials.
This is why I am asking if it "should" work or if it "does" work. And in the 
latter case I would be very much interested in receiving a topology file in 
order to check where exactely is the problem with my topology.
I will try also Gromacs 3.2 anyway.
Bye,

Stefano

---------
School of Applied Chemistry
Curtin University of Technology
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piana at power.curtin.edu.au