<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><DIV>30 mar 2007 kl. 22.32 skrev özge kül:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV>Hi Eric,</DIV> <DIV> </DIV> <DIV>Where is the specbond.dat?After which line is it formed?</DIV></BLOCKQUOTE><DIV><BR class="khtml-block-placeholder"></DIV>specbond.dat is located in <install directory>/share/gromacs/top/</DIV><DIV>I don't understand the question about the line.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>/Erik</DIV><DIV><BR><BLOCKQUOTE type="cite"> <DIV> </DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia"><SPAN><FONT size="3">1.</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="COLOR: fuchsia"><FONT size="3">pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o<SPAN> </SPAN>1ppbfree.gro<SPAN> -merge</SPAN></FONT></SPAN></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><SPAN><SPAN style="FONT-SIZE: 12pt; COLOR: fuchsia; FONT-FAMILY: 'Times New Roman'">2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron</SPAN></SPAN></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia"><SPAN><FONT size="3">3.</FONT><SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="COLOR: fuchsia"><FONT size="3">genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro</FONT></SPAN></FONT></DIV><FONT face="Times New Roman"><SPAN style="COLOR: fuchsia"><FONT size="3"> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><SPAN style="COLOR: fuchsia"><SPAN>4.<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="COLOR: fuchsia">grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top</SPAN></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt 18pt; TEXT-INDENT: -18pt"><SPAN style="COLOR: fuchsia"><SPAN style="FONT-SIZE: 12pt; COLOR: fuchsia; FONT-FAMILY: 'Times New Roman'">5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree-aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr</SPAN></SPAN></DIV></FONT></SPAN></FONT> <DIV>Please help me?:)</DIV> <DIV> </DIV> <DIV>özge</DIV><DIV> <BR class="khtml-block-placeholder"></DIV><HR size="1"><A href="http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com">Bored stiff?</A> Loosen up...<BR><A href="http://us.rd.yahoo.com/evt=49935/*http://games.yahoo.com">Download and play hundreds of games for free</A> on Yahoo! Games.<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. 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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; 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; 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; white-space: normal; widows: 2; word-spacing: 0px; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<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></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<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></SPAN></SPAN></SPAN>+46 18 471 4537<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></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><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></SPAN></SPAN></SPAN>http://xray.bmc.uu.se/molbiophys</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>