[gmx-users] zirconia

[David van der Spoel]

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
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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