<div>hello,</div> <div> i would like to apologise for my hurried attempt to describe my problem earlier.</div> <div>in my hurried attempt i also happened to have attached the wrong topology file.</div> <div>well let me go again and describe what i am tryin to achieve.please do take the patience to look into it.</div> <div> </div> <div>i am a beginner to gromacs and what i am trying to achieve is to see the behaviour of nanosized zirconia particles when sintered.</div> <div>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.</div> <div> </div> <div>i am using buckingham potentials and using the partial ionic model hence the charges -1.35 for oxygen and 2.7 for
zirconium.</div> <div> 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.</div> <div> </div> <div>i checked back with the literature and the values of forces are right.so where could i be going wrong?</div> <div>please do check my topolgy file and see if i am doing any blunder.</div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">;topology file<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ defaults ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>; nbfunc<SPAN style="mso-spacerun: yes"> </SPAN>comb-rule<SPAN style="mso-spacerun:
yes"> </SPAN>gen-pairs<SPAN style="mso-spacerun: yes"> </SPAN>fudgeLJ fudgeQQ<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>no<SPAN style="mso-spacerun: yes"> </SPAN>1.0<SPAN style="mso-spacerun: yes"> </SPAN>1.0<SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in
0pt"><FONT face="Courier New">[ atomtypes ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">;name<SPAN style="mso-spacerun: yes"> </SPAN>mass<SPAN style="mso-spacerun: yes"> </SPAN>charge<SPAN style="mso-spacerun: yes"> </SPAN>ptype<SPAN style="mso-spacerun: yes"> </SPAN>c6<SPAN style="mso-spacerun: yes"> </SPAN><SPAN style="mso-spacerun: yes"> </SPAN>c12<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> O</SPAN>X<SPAN style="mso-spacerun: yes"> 15.9</SPAN>9940<SPAN style="mso-spacerun: yes"> </SPAN>-1.35<SPAN style="mso-spacerun:
yes"> </SPAN>A<SPAN style="mso-spacerun: yes"> </SPAN>2348.3193<SPAN style="mso-spacerun: yes"> </SPAN>0.0547148<SPAN style="mso-spacerun: yes"> </SPAN>51.712e-28<BR><SPAN style="mso-spacerun: yes"> </SPAN>ZR<SPAN style="mso-spacerun: yes"> </SPAN>91.22420<SPAN style="mso-spacerun: yes"> </SPAN>2.70<SPAN style="mso-spacerun: yes"> </SPAN>A<SPAN style="mso-spacerun: yes"> </SPAN>0.0000000<SPAN style="mso-spacerun: yes"> </SPAN>1.0000000<SPAN style="mso-spacerun: yes"> </SPAN>0.0000000<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ nonbond_params ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>; i<SPAN style="mso-spacerun: yes">
</SPAN>j func<SPAN style="mso-spacerun: yes"> </SPAN>a<SPAN style="mso-spacerun: yes"> </SPAN>b<SPAN style="mso-tab-count: 1"> </SPAN>c6<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>OX<SPAN style="mso-spacerun: yes"> </SPAN>OX<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>2348.3193<SPAN style="mso-spacerun: yes"> </SPAN>0.0547148<SPAN style="mso-spacerun: yes"> </SPAN>51.712e-28<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>ZR<SPAN style="mso-tab-count: 1"> </SPAN>OX<SPAN style="mso-spacerun:
yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>9.512e+04<SPAN style="mso-spacerun: yes"> </SPAN>0.0376000<SPAN style="mso-spacerun: yes"> </SPAN>0.0000000<BR><SPAN style="mso-spacerun: yes"> Z</SPAN>R<SPAN style="mso-spacerun: yes"> </SPAN>ZR<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> </SPAN>0.0000000<SPAN style="mso-spacerun: yes"> </SPAN>1.0000000<SPAN style="mso-spacerun: yes"> </SPAN>0.0000000<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ moleculetype ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>ZR 0</FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in
0pt"><o:p><FONT face="Courier New"> </FONT></o:p></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ atoms ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>ZR<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>DP<SPAN style="mso-spacerun: yes"> </SPAN>ZR<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> 2.7</SPAN><SPAN style="mso-spacerun: yes"> </SPAN>91.22420<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Courier New"> </FONT></o:p></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[
moleculetype ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>OX 0</FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Courier New"> </FONT></o:p></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ atoms ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>OX<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>DP<SPAN style="mso-spacerun: yes"> </SPAN>OX<SPAN style="mso-spacerun: yes"> </SPAN>2<SPAN style="mso-spacerun: yes"> -1.35</SPAN><SPAN style="mso-spacerun: yes">
</SPAN>15.99940<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Courier New"> </FONT></o:p></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ system ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">ZIRCONIA<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Courier New"> </FONT></o:p></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">[ molecules ]<o:p></o:p></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">ZR<SPAN style="mso-spacerun: yes"> 1032</SPAN></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New">OX 2064<SPAN style="mso-spacerun: yes"> </SPAN></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN
style="mso-spacerun: yes"></SPAN></FONT> </div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><FONT face="Courier New"><SPAN style="mso-spacerun: yes">thanka a lot for your patience</SPAN></FONT></div> <div class=MsoPlainText style="MARGIN: 0in 0in 0pt"><o:p><FONT face="Courier New"> </FONT></o:p></div> <div> </div><p> 
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