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<DIV dir=ltr align=left><FONT color=#0000ff size=2 face=Arial><SPAN
class=390270016-11092009>I'm re-sending the message below because it seems
to me that it has not arrived to the list.</SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT color=#0000ff size=2 face=Arial><SPAN
class=390270016-11092009>Please forgive me in case of duplicate
sending.</SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT color=#0000ff size=2 face=Arial><SPAN
class=390270016-11092009>Best regards</SPAN></FONT></DIV>
<DIV dir=ltr align=left><FONT color=#0000ff size=2 face=Arial><SPAN
class=390270016-11092009>Anna</SPAN></FONT></DIV><BR>
<DIV dir=ltr lang=it class=OutlookMessageHeader align=left>
<HR tabIndex=-1>
<FONT size=2 face=Tahoma><B>Da:</B> Anna Marabotti
[mailto:anna.marabotti@isa.cnr.it] <BR><B>Inviato:</B> venerdì 11 settembre 2009
14.05<BR><B>A:</B> 'gmx-users@gromacs.org'<BR><B>Oggetto:</B> problems running
REMD on grids<BR></FONT><BR></DIV>
<DIV></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">http://oldwiki.gromacs.org/index.php/REMD</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 oldwww.gromacs.org 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>
<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>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">anna.marabotti@isa.cnr.it</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">http://bioinformatica.isa.cnr.it/anna/anna.htm</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>
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