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
[ 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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