pushyami atluri wrote:
hello,
i would like to apologise for my hurried attempt to describe my problem earlier. in my hurried attempt i also happened to have attached the wrong topology file. well let me go again and describe what i am tryin to achieve.please do take the patience to look into it. i am a beginner to gromacs and what i am trying to achieve is to see the behaviour of nanosized zirconia particles when sintered. initially to start with i have created a box containin two spheres of 4 nm size separated by equilibrium distance .zirconia has body centered tetragonal structure with four oxygen atoms placed in the tetrahedral voids in a criss cross pattern such that no two oxygen atoms lie on the same space diagonal. i am using buckingham potentials and using the partial ionic model hence the charges -1.35 for oxygen and 2.7 for zirconium. the problem that i am encountering is that when i give a run for smaller particles like a 4 nm i get a system which is completely randomised. i checked back with the literature and the values of forces are right.so where could i be going wrong?
please do check my topolgy file and see if i am doing any blunder.
;topology file
[ defaults ]
 ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
2 1 no 1.0 1.0 [ atomtypes ]
;name        mass      charge   ptype            c6           c12
  OX       15.99940     -1.35     A  2348.3193  0.0547148  51.712e-28
   ZR        91.22420      2.70     A  0.0000000  1.0000000  0.0000000
the buckingham parameter can't be right.
for A exp (-B r) + C/r^6
The Zr parameters A 0 and B 1 are weird and the dispersion for O is wrong to. Please note units in gromacs: energy in kJ/mol and distance in nm (chapter 2 in the manual).

[ nonbond_params ]
  ; i    j func           a             b c6
 OX   OX    2    2348.3193   0.0547148       51.712e-28
 ZR   OX    2    9.512e+04     0.0376000       0.0000000
 ZR   ZR    2  0.0000000       1.0000000       0.0000000
[ moleculetype ]
 ZR 0
[ atoms ]
  1    ZR      1     DP     ZR      1   2.7    91.22420
[ moleculetype ]
 OX 0
[ atoms ]
 1     OX      1     DP     OX      2   -1.35    15.99940
[ system ]
ZIRCONIA
[ molecules ]
ZR  1032
OX 2064 thanka a lot for your patience
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
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