<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">The values are in Bohr!<div><br><div><div>On 17 Dec 2013, at 11:26, Chaim Dryzun <<a href="mailto:chaima...@gmail.com">chaima...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">Hello all,<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">I do not understand how the distance function is calculates: the number which are produced by the metadynamics simulation are very different from what I expected.<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">Attached are my input file and the output COLVAR file.<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">The relevant section is:<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">&COLVAR<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman"><span style="mso-spacerun: yes;"> </span>&DISTANCE_FUNCTION<br> <span style="mso-spacerun: yes;"> </span>ATOMS 1 7 2 7<br> <span style="mso-spacerun: yes;"> </span>COEFFICIENT -1.0<br> <span style="mso-spacerun: yes;"> </span>PBC FALSE<br> <span style="mso-spacerun: yes;"> </span>&END DISTANCE_FUNCTION<br> &END COLVAR<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><o:p><font size="3" face="Times New Roman"> </font></o:p></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">At the beginning of the simulation (the reactant state) d(1-7) is 1.513242 Angstrom and d(2-7) is 2.171484 Angstrom so i expected the distance function to be 1.513242 - 2.171484 = -1.132264, but the program returns -2.03441.</font></font></span></div><p style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;" dir="LTR" class="MsoNormal"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font face="Times New Roman"></font></span> </p><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">Generally speaking, I expected the range of this colvar to be from -1.3 up to 1.3, but I get numbers between -3.0 up to 3.0.</font></font></span></div><font size="3" face="Times New Roman"> </font><p style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;" dir="LTR" class="MsoNormal"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font face="Times New Roman"></font></span> </p><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">This prevents me from comparing my results from this simulation with results obtained from other sources.<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><p style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;" dir="LTR" class="MsoNormal"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font face="Times New Roman"></font></span> </p><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">Thanks in advance,<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; line-height: normal; unicode-bidi: embed; direction: ltr;"><span style="font-size: 12pt; mso-fareast-font-family: "Times New Roman"; mso-bidi-font-family: "Times New Roman";"><font><font face="Times New Roman">Chaim Dryzun<o:p></o:p></font></font></span></div><font size="3" face="Times New Roman"> </font><div style="margin: 0cm 0cm 0pt; text-align: left; unicode-bidi: embed; direction: ltr;"><o:p><font size="3" face="Times New Roman"> </font></o:p></div><font size="3" face="Times New Roman"> </font></div><div><br class="webkit-block-placeholder"></div> -- <br> You received this message because you are subscribed to the Google Groups "cp2k" group.<br> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com">cp2k+uns...@googlegroups.com</a>.<br> To post to this group, send email to <a href="mailto:cp...@googlegroups.com">cp...@googlegroups.com</a>.<br> Visit this group at <a href="http://groups.google.com/group/cp2k">http://groups.google.com/group/cp2k</a>.<br> For more options, visit <a href="https://groups.google.com/groups/opt_out">https://groups.google.com/groups/opt_out</a>.<br> <span><COLVAR.dat></span><span><META.inp></span></blockquote></div><br></div></body></html>