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<BR> <SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Hi,</FONT></FONT></SPAN><BR>
<P class=ecxMsoNormal><SPAN 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.</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN 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 lang=EN-GB><FONT size=3>“</FONT></SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu">The options </SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusMonL-Regu">-pi</SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu">, </SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusMonL-Regu">-po</SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu">, </SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusMonL-Regu">-pd</SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu">, </SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusMonL-Regu">-pn </SPAN><SPAN lang=EN-GB style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu">are used for potential of mean force calculations and umbrella sampling. </SPAN><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu">See manual.”</SPAN></FONT></P>
<P class=ecxMsoNormal><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: NimbusRomNo9L-Regu"><FONT face="Times New Roman"> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN 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):</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=FR><FONT size=3><FONT face="Times New Roman">source /gpfs/apps/GROMACS/gromacs-4.0.2/bin/GMXRC</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN 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</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">gzip NA-0.0250.pdo</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><FONT size=3><FONT face="Times New Roman"><SPAN lang=EN-GB>Being </SPAN><SPAN lang=PT-BR>NA-0.0250.ppa:</SPAN></FONT></FONT></P>
<P class=ecxMsoNormal><SPAN lang=PT-BR><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><FONT size=3><FONT face="Times New Roman">verbose<SPAN> </SPAN>= yes</FONT></FONT></P>
<P class=ecxMsoNormal><FONT size=3><FONT face="Times New Roman">runtype<SPAN> </SPAN>= umbrella<SPAN> </SPAN></FONT></FONT></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">pulldim<SPAN> </SPAN>= N N Y<SPAN> </SPAN></FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">reftype<SPAN> </SPAN>= com<SPAN> </SPAN></FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">reference_group = UNK<SPAN> </SPAN></FONT></FONT></SPAN></P>
<P class=ecxMsoNormal>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman"></FONT></FONT></SPAN></P><SPAN lang=PT-BR><FONT size=3><FONT face="Times New Roman">group_1<SPAN> </SPAN>= Na_-0.025</FONT></FONT></SPAN>
<BR>
<P class=ecxMsoNormal><SPAN lang=PT-BR><FONT size=3><FONT face="Times New Roman">K1<SPAN> </SPAN>= 970.86;<SPAN> </SPAN>; kJ / (mol nm^2)</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Pos1<SPAN> </SPAN>= 0.000 0.000 -0.025<SPAN> </SPAN>; centre of the umbrella potential</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN 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.</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN 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.</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN 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?</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Thank you very much for your help.</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Best wishes,</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Rebeca Garcia.</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Santiago de Compostela University</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT size=3><FONT face="Times New Roman">Spain.</FONT></FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P>
<P class=ecxMsoNormal><SPAN lang=EN-GB><FONT face="Times New Roman" size=3> </FONT></SPAN></P> <BR><BR>
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