Hi Hiromichi,<br><br>It is likely that you have some groups which are not covered by "Protein" and "Other". You can use "Protein" and "Non-Protein" in stead. But make sure that the two groups correspond to two distinct groups in your system. You may run into trouble if you have some non-standard residue in your protein which will end up in the "Non-Protein" group.
<br><br>Cheers,<br><br>Tsjerk<br><br><div><span class="gmail_quote">On 6/14/06, <b class="gmail_sendername">Hiromichi Tsurui</b> <<a href="mailto:tsurui@med.juntendo.ac.jp">tsurui@med.juntendo.ac.jp</a>> wrote:</span>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>
<div bgcolor="#ffffff">
<div><font face="MS UI Gothic" size="2">
</font><p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3">Dear all;</font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3"> </font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><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).</font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><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;</font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3">"Fatal error.</font></font></span></p>
<p style="margin: 0mm 0mm 0pt; text-indent: 10.5pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3">Not enough ref_t and tau_t values."</font></font></span></p>
<p style="margin: 0mm 0mm 0pt; text-indent: 10.5pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3">How should I change the conditions ?</font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3"></font></font></span><font face="MS UI Gothic" size="2"> </font></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3"><font face="MS UI Gothic">Many thanks for your help.</font> <font face="MS UI Gothic"> </font></font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font face="MS UI Gothic"></font></font></span><font face="MS UI Gothic" size="2"> </font></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3"> </font></font></span></p>
<p style="margin: 0mm 0mm 0pt;"><span lang="EN-US"><font face="MS UI Gothic" size="2"><font size="3">cpp<span>
</span>=<span> </span>/lib/cpp<br>define<span>
</span>=<span> </span><br>integrator<span>
</span>=<span> </span>md<br>tinit<span>
</span>=<span> </span>0.0<br>dt<span>
</span>=<span> </span>0.002<span> </span><br>nsteps<span>
</span>=<span> </span>100000<span> </span><br>nstcomm<span>
</span>=<span> </span>1<br>nstxout<span>
</span>=<span> </span>50000<br>nstvout<span>
</span>=<span> </span>50000<br>nstfout<span>
</span>=<span> </span>0<br>nstlog<span>
</span>=<span> </span>10000<br>nstenergy<span>
</span>=<span> </span>250<br>nstxtcout<span>
</span>=<span>
</span>10000<br>xtc_precision<span> </span>=<span> </span>1000<br>xtc_grps<span>
</span>=<span> </span>Protein<br>energygrps<span>
</span>=<span> </span>Protein
other<br>nstlist<span>
</span>=<span> </span>5<br>ns_type<span>
</span>=<span> </span>grid<br>pbc<span>
</span>=<span> </span>xyz<br>rlist<span>
</span>=<span> </span>0.9<br>coulombtype<span>
</span>=<span>
</span>Reaction-Field<br>epsilon_r<span>
</span>=<span> </span>78.0<br>rcoulomb<span>
</span>=<span> </span>1.4<br>vdw-type<span>
</span>=<span> </span>Cut-off<br>rvdw<span>
</span>=<span> </span>1.4<br>tcoupl<span>
</span>=<span> </span>Berendsen<br>tc-grps<span> </span><span> </span>=<span> </span>Protein other<br>ref_t<span>
</span>=<span> </span>300 300<br>tau_t<span>
</span>=<span> </span>0.1 0.1<br>pcoupl<span>
</span>=<span> </span>Berendsen<br>tau_p<span>
</span>=<span>
</span>1.0<br>compressibility<span> </span>=<span> </span>4.6e-5<br>ref_p<span>
</span>=<span> </span>1.0<br>gen-vel<span>
</span>=<span> </span>yes<br>gen-temp<span>
</span>=<span> </span>300<br>gen-seed<span>
</span>=<span>
</span>$RANDOM<br>constraints<span>
</span>=<span>
</span>all-bonds<br> </font></font></span></p></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" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">tsurui@med.juntendo.ac.jp</a></font></div></div>
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</a><br><br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen
<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>