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<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial","sans-serif"'>I
am running NPT simulations by using Parrinello-Rahman pressure coupling on Gromacs
3.3.3. My system contains epoxy and cross-linker molecules. By
modifying the topology file (add bond, angle, torsion terms in topology), all
the molecules are connected together to be an huge polymeric molecule. The
MD jobs were running well before and after polymerization. However, while
analyzing the data by using g_rdf, it keeps showing the message “There
were XXX inconsistent shifts. Check your topology” for the structures
after polymerization and the g(r) are not reasonable. Does anyone have
any idea about this issue? I am also curious about how g_rdf deal
with “inconsistent shifts.” Does g_rdf ignore those data or
do something else?<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial","sans-serif"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial","sans-serif"'>Thanks,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:12.0pt;font-family:"Arial","sans-serif"'>Po-Han<o:p></o:p></span></p>
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