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<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">Hi,<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><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">I am trying to calculate the PMF of an ion with Gromacs 4. I have read in the Gromacs list that the pull code had been completely rewritten in the new version of Gromacs, but I cannot find much information about the new way to use this.<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">Reading the manual (pag 280) I can see: </FONT></FONT></SPAN><FONT face="Times New Roman"><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3>“</FONT></SPAN><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusRomNo9L-Regu" lang=EN-GB>The options </SPAN><SPAN style="FONT-FAMILY: NimbusMonL-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusMonL-Regu" lang=EN-GB>-pi</SPAN><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusRomNo9L-Regu" lang=EN-GB>, </SPAN><SPAN style="FONT-FAMILY: NimbusMonL-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusMonL-Regu" lang=EN-GB>-po</SPAN><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusRomNo9L-Regu" lang=EN-GB>, </SPAN><SPAN style="FONT-FAMILY: NimbusMonL-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusMonL-Regu" lang=EN-GB>-pd</SPAN><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusRomNo9L-Regu" lang=EN-GB>, </SPAN><SPAN style="FONT-FAMILY: NimbusMonL-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusMonL-Regu" lang=EN-GB>-pn </SPAN><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-ansi-language: EN-GB; mso-bidi-font-family: NimbusRomNo9L-Regu" lang=EN-GB>are used for potential of mean force calculations and umbrella sampling. </SPAN><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-bidi-font-family: NimbusRomNo9L-Regu">See manual.”<o:p></o:p></SPAN></FONT></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="FONT-FAMILY: NimbusRomNo9L-Regu; FONT-SIZE: 10pt; mso-bidi-font-family: NimbusRomNo9L-Regu"><o:p><FONT face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">So, I prepared a tpr and a .ppa file and tried the calculation and used (for example for one window):<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: FR" lang=FR><FONT size=3><FONT face="Times New Roman">source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: PT-BR" lang=PT-BR><FONT size=3><FONT face="Times New Roman">srun -n 8 mdrun_s -v -stepout 1000 -s NA-0.0250.tpr -pi NA-0.0250.ppa -po pullout.ppa -pn NA-0.0250.ndx -pd -deffnm NA-0.0250<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">gzip NA-0.0250.pdo<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><FONT size=3><FONT face="Times New Roman"><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB>Being </SPAN><SPAN style="mso-ansi-language: PT-BR" lang=PT-BR>NA-0.0250.ppa:<o:p></o:p></SPAN></FONT></FONT></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: PT-BR" lang=PT-BR><o:p><FONT size=3 face="Times New Roman"> </FONT></o:p></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><FONT size=3><FONT face="Times New Roman">verbose<SPAN style="mso-spacerun: yes"> </SPAN>= yes<o:p></o:p></FONT></FONT></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><FONT size=3><FONT face="Times New Roman">runtype<SPAN style="mso-spacerun: yes"> </SPAN>= umbrella<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">pulldim<SPAN style="mso-spacerun: yes"> </SPAN>= N N Y<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">reftype<SPAN style="mso-spacerun: yes"> </SPAN>= com<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">reference_group = UNK<SPAN style="mso-spacerun: yes"> </SPAN></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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><SPAN style="mso-ansi-language: PT-BR" lang=PT-BR><FONT size=3><FONT face="Times New Roman">group_1<SPAN style="mso-spacerun: yes"> </SPAN>= Na_-0.025<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: PT-BR" lang=PT-BR><FONT size=3><FONT face="Times New Roman">K1<SPAN style="mso-spacerun: yes"> </SPAN>= 970.86;<SPAN style="mso-spacerun: yes"> </SPAN>; kJ / (mol nm^2)<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Pos1<SPAN style="mso-spacerun: yes"> </SPAN>= 0.000 0.000 -0.025<SPAN style="mso-spacerun: yes"> </SPAN>; centre of the umbrella potential<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">I don´t get any errors during the calculation, however, I did not get any out files such as *.pdo.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">I only get the *cpt, *trr, *log and *edr files after the calculation, but no signal of *pdo.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Does anyboy had used Gromacs 4 for calculating PMF? Am I doing something wrong?<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Thank you very much for your help.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Best wishes,<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Rebeca Garcia.</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Santiago de Compostela University</FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" class=MsoNormal><SPAN style="mso-ansi-language: EN-GB" lang=EN-GB><FONT size=3><FONT face="Times New Roman">Spain.<o:p></o:p></FONT></FONT></SPAN></P>
<P style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none" 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; mso-layout-grid-align: none" 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>
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