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<DIV><FONT size=2 face=Arial> <SPAN style="mso-ansi-language: EN-GB"
lang=EN-GB><FONT size=3><FONT face=Calibri>Dear Gromacs People<?xml:namespace
prefix = o ns = "urn:schemas-microsoft-com:office:office"
/><o:p></o:p></FONT></FONT></SPAN>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><o:p><FONT size=3
face=Calibri></FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face=Calibri>I am
working about md simulations of a linear polymer chain in water at high
hydration degree. The force field is G45a3, SPC water, NPT ensemble, gromacs
4.5.3.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face=Calibri>I
acquired a 50 ns trajecory ( time step 2 fs, all bonds constrained with LINCS,
PME, T=293 K, P= 1 atm ) with absolutely no problem using gromacs in serial on
my PC.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face=Calibri>Therefore I was very surprised when, trying to repeat exactly the
same simulation on another computer where mdrun works in parallel (with MPI),
the molecular dynamics calculation could not
start.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face=Calibri>Even
working on only 2 nodes, the run crashes at the first step, returning a long
list of LINCS errors and an infinite system
energy.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face=Calibri>Firstly I verified that the processed topology after grompp was the
same on the two machines.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face=Calibri>Then
I tried the parallel run using particle decomposition instead of domain
decomposition, without success.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face=Calibri>The
starting configuration was energy minimized to a maximum force of 90
kJmol-1nm-1. Is this value too high for a parallel
simulation?</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face=Calibri>I
can provide information about the mdp file and the mdrun errors of my
parallel simulation, in case.</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3 face=Calibri>Thanks in
advance for any suggestion.<o:p></o:p></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face=Calibri>Ester</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN
style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT
face=Calibri><o:p></o:p></FONT></FONT></SPAN> </P></FONT></SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial>Ester Chiessi<BR>Dipartimento di Scienze e
Tecnologie Chimiche<BR>Università di Roma Tor Vergata<BR>Via della Ricerca
Scientifica<BR>00133 Roma<BR><A
href="http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm">http://www.stc.uniroma2.it/cfmacro/cfmacroindex.htm</A><BR>tel:
*39*6*72594462</FONT></DIV></BODY></HTML>