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<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>On
Wed, 2004-06-09 at 03:15, F Jiang wrote:<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
Dear gmx-users,<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
Thanks for the previous replies. The b__topb__ command shows the CPU is<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
~0% user ~100% system. I get this problem when mdrun_pr goes on<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
forever (>2000mins CPU) and when there are many LINCS warnings and<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
huge bond deviations. I tried b__lincs_order=50 with l-bfgs and then<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
mdrun_pr (with a few initial steps generating LINCS warnings) and<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
mdrun_md could run. Should I also increase b__lincs_iter? In any case,<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
I would think LINCS should abort instead of running for too long.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>avoid
using constraints with minimization.<o:p></o:p></span></font></p>
<p class=MsoNormal align=left style='text-align:left;text-autospace:none'><font
size=2 face=Arial><span lang=EN-US style='font-size:10.0pt;font-family:Arial'>>
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Sorry David, I didn’t use constraints with minimization.
I meant to say I got LINCS warnings when running mdrun_pr and it sometimes ran for
a very long time. After increasing lincs_order, mdrun_pr seemed to be ok. And mdrun_md
will run. Whether I’m doing meaningful things is another question, my starting
structures have many bad geometries. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=1 face=Arial><span lang=EN-US style='font-size:
9.0pt;font-family:Arial'>Thanks again---Fan<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span lang=EN-US><o:p> </o:p></span></font></p>
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