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<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT
size=3>Dear all;<?xml:namespace prefix = o ns =
"urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><o:p><FONT
size=3> </FONT></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT size=3>I
am trying to calculate the binding free energy of an MHC-molecule and a peptide
by thermodynamic integration method. The system contains binding domain of MHC
molecule, a peptide presented on it, water-molecules (about 13,000), and ions
(Na+ and Cl- at PBS-concentration).<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT
size=3>After energy minimization, I tried to equilibrate the system with the
mdp-file as follows, and an error-message appeared as
such;<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT
size=3>“Fatal error.<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText
style="MARGIN: 0mm 0mm 0pt; TEXT-INDENT: 10.5pt; mso-char-indent-count: 1.0"><SPAN
lang=EN-US style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT
size=3>Not enough ref_t and tau_t values.”<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText
style="MARGIN: 0mm 0mm 0pt; TEXT-INDENT: 10.5pt; mso-char-indent-count: 1.0"><SPAN
lang=EN-US style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT
size=3>How should I change the conditions ?<o:p></o:p></FONT></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><o:p><FONT
size=3></FONT></o:p></SPAN> </P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><o:p><FONT
size=3><FONT face="MS UI Gothic">Many thanks for your help.</FONT> <FONT
face="MS UI Gothic"> </FONT></FONT></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><o:p><FONT
face="MS UI Gothic"></FONT></o:p></SPAN> </P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><o:p><FONT
size=3> </FONT></o:p></SPAN></P>
<P class=MsoPlainText style="MARGIN: 0mm 0mm 0pt"><SPAN lang=EN-US
style="FONT-FAMILY: 'ＭＳ ゴシック'; mso-bidi-font-family: 'ＭＳ ゴシック'"><FONT
size=3>cpp<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>/lib/cpp<BR>define<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN><BR>integrator<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>md<BR>tinit<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.0<BR>dt<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.002<SPAN
style="mso-spacerun: yes"> </SPAN><BR>nsteps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>100000<SPAN
style="mso-spacerun: yes"> </SPAN><BR>nstcomm<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>1<BR>nstxout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>50000<BR>nstvout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>50000<BR>nstfout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0<BR>nstlog<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>10000<BR>nstenergy<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>250<BR>nstxtcout<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>10000<BR>xtc_precision<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>1000<BR>xtc_grps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>Protein<BR>energygrps<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>Protein
other<BR>nstlist<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>5<BR>ns_type<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>grid<BR>pbc<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>xyz<BR>rlist<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.9<BR>coulombtype<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>Reaction-Field<BR>epsilon_r<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>78.0<BR>rcoulomb<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>1.4<BR>vdw-type<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>Cut-off<BR>rvdw<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>1.4<BR>tcoupl<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>Berendsen<BR>tc-grps<SPAN
style="mso-spacerun: yes"> </SPAN><SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>Protein other<BR>ref_t<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>300 300<BR>tau_t<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>0.1 0.1<BR>pcoupl<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>Berendsen<BR>tau_p<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>1.0<BR>compressibility<SPAN
style="mso-spacerun: yes"> </SPAN>=<SPAN
style="mso-spacerun: yes"> </SPAN>4.6e-5<BR>ref_p<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>1.0<BR>gen-vel<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>yes<BR>gen-temp<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes"> </SPAN>300<BR>gen-seed<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>$RANDOM<BR>constraints<SPAN
style="mso-spacerun: yes">
</SPAN>=<SPAN style="mso-spacerun: yes">
</SPAN>all-bonds<BR><o:p> </o:p></FONT></SPAN></P></FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2>Hiromichi Tsurui MD, PhD<BR>Dept.
Pathology, <BR>Juntendo
University<BR>Phone:81-3-5802-1039<BR>Fax:81-3-3813-3164<BR><A
href="mailto:tsurui@med.juntendo.ac.jp">tsurui@med.juntendo.ac.jp</A></FONT></DIV></BODY></HTML>