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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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