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<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Hello,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">I want to simulate a membrane+proteína system (more than 700.000 atoms) with Gromacs 4 and I would like to use 512 proc.<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">I am creating the mdp file with Gromacs 3, since I have read in the wiki that it was a good way to include the number or processors ins the mdp file for the new version.<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">For grompp with Gromacs 3.3 I amincluding this options <SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">in the input mdp file:<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P></FONT></FONT></FONT></SPAN>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3></FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">fourierspacing<SPAN style="mso-spacerun: yes"> </SPAN>= 0.12</FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">fourier_nx<SPAN style="mso-spacerun: yes"> </SPAN>= 1024<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">fourier_ny<SPAN style="mso-spacerun: yes"> </SPAN>= 1024<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">fourier_nz<SPAN style="mso-spacerun: yes"> </SPAN>= 0<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt">
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3></FONT></o:p></SPAN></P><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">but when I execute:<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3></FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">grompp -f equilibrado2.mdp -c equilibrado.gro -p para_equilibrado.top -o equilibrado2.tpr -n index.ndx -np 512<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">I receive this error:<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">-------------------------------------------------------<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Program grompp, VERSION 3.3.3<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Source code file: grompp.c, line: 1021<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Fatal error:<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">invalid number of nodes 512<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">-------------------------------------------------------<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=PT-BR style="mso-ansi-language: PT-BR"><o:p><FONT face="Times New Roman" color=#000000 size=3></FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">When I had tried the same with 256 proc, using fourier_nx= fourier_ny=512, the correspondent error did not appear.<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Is there a limit of processors in Gromacs for grompp or which could be the problem?<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><FONT size=3><FONT color=#000000><FONT face="Times New Roman">Thank you very much for your help in advance,<o:p></o:p></FONT></FONT></FONT></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN lang=EN-GB style="mso-ansi-language: EN-GB"><o:p><FONT face="Times New Roman" color=#000000 size=3> </FONT></o:p></SPAN></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" color=#000000 size=3>Rebeca García Fandiño</FONT></P>
<P class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" color=#000000 size=3>Parc Cientific of Barcelona</FONT></P><br /><hr />¿Todavía no conoces El Duelo? Descúbrelo y reta a tus contactos de Messenger <a href='http://www.vivelive.com/duelo' target='_new'>El Duelo</a></body>
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