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<p class=MsoPlainText>Hi Friends<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>I was trying to buid <span style='color:#00B0F0'>Gromacs
3.3.1 64-bit on NATIVE Windows 2003 Server RC2 (AMD 64 Bit Optron) with VS
2005.</span><o:p></o:p></p>
<p class=MsoPlainText>The projects are getting build perfectly w/o any error.<o:p></o:p></p>
<p class=MsoPlainText>But I have some <span style='color:#00B0F0'>RUN TIME
ERROR while testing the binaries (*.exe) with the demo.pl file</span><o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>1. <span style='color:red'>The program
"genbox" does generates the "temp.top" file and tries to
rename it "cpeptide.top". But it is not able to rename the file as
the folder contains another "cpeptide.top" file. But this behaviour
is NOT seen in 32-bit of UNIX.</span> <o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText># The source files are: gmx_genbox.c (Line: 557) and
gmx_genion.c (Line: 287)<o:p></o:p></p>
<p class=MsoPlainText># Code snipset...<o:p></o:p></p>
<p class=MsoPlainText>---------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoPlainText>fclose(fpin);<o:p></o:p></p>
<p class=MsoPlainText>fclose(fpout);/* use ffopen to generate backup of
topinout */<o:p></o:p></p>
<p class=MsoPlainText>fpout=ffopen(topinout,"w");<o:p></o:p></p>
<p class=MsoPlainText>fclose(fpout);<o:p></o:p></p>
<p class=MsoPlainText>remove(topinout);//My Change<o:p></o:p></p>
<p class=MsoPlainText>rename(TEMP_FILENM,topinout);<o:p></o:p></p>
<p class=MsoPlainText>---------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText># Then I have added the line before these as:
remove(topinout); So that the updated "temp.top" file will be renamed
to "cpeptide.top"<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>2. <span style='color:red'>The second problem is
due to invalid range value (ci) in file: nsgrid.c (Line: 225 & Line: 277)<o:p></o:p></span></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText># The out put is like ....<o:p></o:p></p>
<p class=MsoPlainText>-------------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoPlainText>"Program mdrun, VERSION 3.3.1<o:p></o:p></p>
<p class=MsoPlainText>Source code file: ..\..\..\src\mdlib\nsgrid.c, line: 228<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Range checking error:<o:p></o:p></p>
<p class=MsoPlainText>Explanation: During neighborsearching, we assign each
particle to a grid<o:p></o:p></p>
<p class=MsoPlainText>based on its coordinates. If your system contains
collisions or parameter<o:p></o:p></p>
<p class=MsoPlainText>errors that give particles very high velocities you might
end up with some<o:p></o:p></p>
<p class=MsoPlainText>coordinates being +-Infinity or NaN (not-a-number).
Obviously, we cannot<o:p></o:p></p>
<p class=MsoPlainText>put these on a grid, so this is usually where we detect
those errors.<o:p></o:p></p>
<p class=MsoPlainText>Make sure your system is properly energy-minimized and
that the potential<o:p></o:p></p>
<p class=MsoPlainText>energy seems reasonable before trying again.<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Variable ci has value -2147483648. It should have been
within [ 0 .. 96 ]<o:p></o:p></p>
<p class=MsoPlainText>Please report this to the mailing list
(gmx-users@gromacs.org)<o:p></o:p></p>
<p class=MsoPlainText>------------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText># This may be due to pointer assignment at line: 213 and
the int variable ci is not able to initialize properly.<o:p></o:p></p>
<p class=MsoPlainText># Code snipset is ....<o:p></o:p></p>
<p class=MsoPlainText>------------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoPlainText>.....<o:p></o:p></p>
<p class=MsoPlainText>int *cell_index=grid->cell_index;<o:p></o:p></p>
<p class=MsoPlainText>.....<o:p></o:p></p>
<p class=MsoPlainText>for(i=CG0[m]; (i<CG1[m]); i++) {<o:p></o:p></p>
<p class=MsoPlainText>ci = cell_index[i]; // Hear ci is not properly
assigned to valid integer value<o:p></o:p></p>
<p class=MsoPlainText>range_check(ci,0,ncells);<o:p></o:p></p>
<p class=MsoPlainText>.....<o:p></o:p></p>
<p class=MsoPlainText>}<o:p></o:p></p>
<p class=MsoPlainText>------------------------------------------------------------------------------<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>So, can anybody plz help me to solve this problems for
native 64-bit Windows platform using VS 2005 ?<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Thank you<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
<p class=MsoPlainText>Thank You;<o:p></o:p></p>
<p class=MsoPlainText>URPradhan At Gmail Dot Com<o:p></o:p></p>
<p class=MsoPlainText><o:p> </o:p></p>
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