[gmx-users] zirconia

pushyami atluri shims88 at yahoo.co.in
Tue May 22 20:28:51 CEST 2007

   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
  [ 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 ]
  [ molecules ]
  ZR  1032
  OX  2064  
  thanka a lot for your patience

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