<html><body bgcolor="#FFFFFF"><div>Did you try to remove the "_" from your file name?<br><br>On Sep 11, 2009, at 14:04, Anna Marabotti <<a href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div>
<div><font size="2" face="Arial">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman">Dear gmx-users,<o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3" face="Times New Roman">I’m trying to perform some REMD calculations<span class="593555311-11092009"> with GROMACS 4.0.5</span>, and I found on the Wiki
site these instructions:</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman"><o:p></o:p></font></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman"><a href="http://oldwiki.gromacs.org/index.php/REMD"><a href="http://oldwiki.gromacs.org/index.php/REMD">http://oldwiki.gromacs.org/index.php/REMD</a></a></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman"><o:p></o:p></font></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman">that I’m trying to follow, but I encountered some
problems.<o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font face="Times New Roman"><font size="3">If I understand well the instructions, if I want to perform replicas at N
different temperatures, I have to create N different .mdp files and then N
different .tpr files, that I should name “filename”_0, “filename”_1...<span class="593555311-11092009"> "</span>filename”_N-1. That’s what I did: I created 16
different .mdp files and 16 .tpr files that I called REMD_0.tpr. REMD_1.tpr
REMD_2.tpr ... REMD_15.tpr. At this point, I have to launch the mdrun command
with the –multi, -replex (optionally, -reseed) options. <span class="593555311-11092009">Following the example in "Execution
step", </span>my command line should
be:<o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman">mdrun –s REMD_.tpr –multi 16 –replex 1000 –deffnm
REMD_<span style="mso-spacerun: yes"> </span>-np
16<o:p></o:p></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font face="Times New Roman"><font size="3"><span class="593555311-11092009">That's what I did, but </span>I
experienced some difficulties on the parallel machines <span class="593555311-11092009">that </span>I’m using to perform simulations. In
particular, I inserted the <span class="593555311-11092009">above
</span>command into a script t<span class="593555311-11092009">hat is used on the
machine to</span> launch <span class="593555311-11092009">the
</span>program<span class="593555311-11092009"> in an interactive
way</span>, <span class="593555311-11092009">but</span> GROMACS returns an
error saying that “cannot open file REMD_.tpr” (and in fact, the file REMD_.tpr
does not exist, only files REMD_0.tpr, REMD_1.tpr etc do exist!)<span class="593555311-11092009"> I also retried launching the same command from the
shell, but the error was the same.</span></font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3"><font face="Times New Roman">So my question is: how does GROMACS “understand” that it
has to interpret “REMD_.tpr” not as a single file, but as a group of files
indexed _0, _1, _2 and so on? Does it depend on the order of the options? Could
you please give me some hints about?</font></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3" face="Times New Roman"><o:p><span class="593555311-11092009"></span></o:p></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3" face="Times New Roman"><o:p><span class="593555311-11092009">BTW, another problem:
I tried to find solution searching in the <a href="http://oldwww.gromacs.org">oldwww.gromacs.org</a> site, but I am
still unable to consult the gmx-users archives using a keyword as it was
possible in the past. How can I find information in the GROMACS
archives?</span></o:p></font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3" face="Times New Roman"><o:p><span class="593555311-11092009"></span></o:p></font></span> </p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3" face="Times New Roman"><o:p><span class="593555311-11092009">Many thanks and
regards</span></o:p></font></span></p>
</font><p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><font size="2" face="Arial"><span style="mso-ansi-language: EN-GB" lang="EN-GB"><font size="3" face="Times New Roman"><o:p><span class="593555311-11092009">Anna</span></o:p></font></span></font></p></div>
<div align="left"><font size="2" face="Arial">____________________________________________________</font></div>
<div align="left"><font size="2" face="Arial">Anna Marabotti, Ph.D.</font></div>
<div align="left"><font size="2" face="Arial">Laboratory of Bioinformatics and
Computational Biology</font></div>
<div align="left"><font size="2" face="Arial">Institute of Food Science,
CNR</font></div>
<div align="left"><font size="2" face="Arial">Via Roma, 64</font></div>
<div align="left"><font size="2" face="Arial">83100 Avellino (Italy)</font></div>
<div align="left"><font size="2" face="Arial">Phone: +39 0825 299651</font></div>
<div align="left"><font size="2" face="Arial">Fax: +39 0825 781585</font></div>
<div align="left"><font size="2" face="Arial">Email: <a href="mailto:anna.marabotti@isa.cnr.it"><a href="mailto:anna.marabotti@isa.cnr.it">anna.marabotti@isa.cnr.it</a></a></font></div>
<div align="left"><font size="2" face="Arial">Skype account: annam1972</font></div>
<div align="left"><font size="2" face="Arial">Web page: <a href="http://bioinformatica.isa.cnr.it/anna/anna.htm"><a href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</a></a></font></div>
<div align="left"><font size="2" face="Arial"></font> </div>
<div align="left"><font size="2" face="Arial">"If you think you are too small to make
a difference, try sleeping with a mosquito"</font></div>
<div> </div>
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