<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><DIV>On 29/ago/07, at 04:11, Mark Abraham wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dear all,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Using</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">g_angle -f ../trj1_0_100.xtc -s ../g_prot.tpr -n test.ndx -or -type</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">dihedral -e 10000</DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">g_covar -f traj.trr -s dummy.gro -nofit</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">It seems like the trajectory is of a different length, because a</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">different timestep seems to be used:</DIV> </BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Well, you are using a different trajectory file...</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV><DIV>It is different because it is made of angles, not of coordinates. But the length, the numbers of frames and the timestep should be the same. Shouldn't it?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Fabio</DIV><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Mark</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; 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border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">----</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Fabio Affinito, PhD</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">SISSA/ISAS - Statistical and Biological Physics</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><BR class="khtml-block-placeholder"></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Via Beirut, 4<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN><SPAN class="Apple-style-span" style="white-space: pre; ">email: <A href="mailto:affinito@sissa.it">affinito@sissa.it</A></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; ">3</SPAN></SPAN><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; ">4014 Trieste</SPAN></SPAN><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN><SPAN class="Apple-style-span" style="white-space: pre; ">phone: +39 040 3787 303</SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: normal;">ITALY<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN>fax: +39 040 3787 528</SPAN></SPAN></SPAN></SPAN></DIV><DIV style="margin-top: 0px; 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