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<TITLE>Help: How to reset &quot;normalizeconfiguration()&quot; in the example &quot;MolecularDynamics/solvation.py&quot;</TITLE>
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<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">Hello:</FONT></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">I am using the windows version of MMTk.</FONT></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">When I try</FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">the example MolecularDynamics/solvation.py</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">,</FONT><FONT SIZE=2 FACE="&#23435;&#20307;"> I</FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">find that the line</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">:</FONT></SPAN><SPAN LANG="en-us"></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">**********************************</FONT></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT COLOR="#FF0000" SIZE=2 FACE="&#23435;&#20307;">protein.normalizeConfiguration()</FONT></SPAN><SPAN LANG="en-us"></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">**********************************</FONT></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">d</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">oes</FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">not</FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">work soundly</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">:</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;"></FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">the</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;"> program</FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">can not</FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">run pro</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">per</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">ly</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;"></FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">w</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">ith</FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">it</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">,</FONT><FONT SIZE=2 FACE="&#23435;&#20307;"></FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">while wit</FONT><FONT SIZE=2 FACE="&#23435;&#20307;">hout it the</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;"> protein</FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">molecule</FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">will lies out of the water box</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;"></FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">center</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">.</FONT></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">H</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">ope</FONT> <FONT SIZE=2 FACE="&#23435;&#20307;">someone can tell me how to set the function</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;"></FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">&quot;</FONT></SPAN><SPAN LANG="en-us"><FONT COLOR="#FF0000" SIZE=2 FACE="&#23435;&#20307;"></FONT></SPAN><SPAN LANG="en-us"> <FONT COLOR="#FF0000" SIZE=2 FACE="&#23435;&#20307;">protein.normalizeConfiguration()</FONT></SPAN><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">&quot;</FONT><FONT SIZE=2 FACE="&#23435;&#20307;"></FONT></SPAN><SPAN LANG="en-us"> <FONT SIZE=2 FACE="&#23435;&#20307;">rightly.</FONT></SPAN><SPAN LANG="en-us"></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">Any clues as to how to rectify this problem would be greatly appreciated.</FONT></SPAN></P>

<P ALIGN=LEFT><SPAN LANG="en-us"><FONT SIZE=2 FACE="&#23435;&#20307;">Bin Gu</FONT></SPAN><SPAN LANG="en-us"></SPAN></P>

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