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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Yanmei,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I had this problem with water molecules, and I found that any
time I changed the constrains without changing the boxes I generated through ‘editconf’.
So, after changing the constrains, I had to redo all my box generation process,
then it was fine. But I ran into another problem and that was I had a separate row
of molecules out of my box (which I do not know where they come from)!<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Payman<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On
Behalf Of </b>Yanmei Song<br>
<b>Sent:</b> May 7, 2009 6:06 PM<br>
<b>To:</b> gmx-users@gromacs.org<br>
<b>Subject:</b> [gmx-users] Some molecules disconnected into many parts after
EM<o:p></o:p></span></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<p class=MsoNormal>Dear users:<br>
<br>
I set up a 8nm cubic box with 6 long chain molecules. After EM, there is no
error message. However I found that in the gro file by visualization, 2 of the
chains has been split in many parts, which means many bonds in the molecules
disconnected. And also the other 4 are good. I checked em.log and eveyting
looks fine.<br>
<br>
Steepest Descents converged to machine precision in 1545 steps,<br>
but did not reach the requested Fmax < 10.<br>
Potential Energy = -7.51461594735782e+03<br>
Maximum force = 2.66505909651672e+02 on atom 1256<br>
Norm of force = 9.84300153087768e+00<br>
<br>
Anyone knows how to solve the problem? Thanks in advance!<br clear=all>
<br>
-- <br>
Yanmei Song<br>
Department of Chemical Engineering<br>
ASU<o:p></o:p></p>
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