<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><FONT face="Times New Roman" size=3>dear sir/Madam </FONT> </DIV>
<P class=MsoNormal style="MARGIN: 5pt 0in"><FONT face="Times New Roman" size=3>i want to work in mopac/gromacs interface for that i have downloaded mopac 7-1.10 tar.gz when run ./configure in the TAR file in command prompt of redhat linux EL5 to install mopac</FONT>
<P class=MsoNormal style="MARGIN: 5pt 0in"><FONT face="Times New Roman" size=3> i got the the following error in command prompt </FONT>
<P class=MsoNormal style="MARGIN: 5pt 0in"><FONT face="Times New Roman"><B><SPAN style="FONT-SIZE: 10pt">bash: ./configure: /bin/sh^M: bad interpreter: No such file or directory</SPAN></B><SPAN style="FONT-SIZE: 10pt"></SPAN></FONT>
<P class=MsoNormal style="MARGIN: 5pt 0in"><FONT face="Times New Roman"><SPAN> please kindly rectify the error in the configure file i am waiting for your reply</SPAN></FONT></DIV>
<DIV>thanks in Advance</DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV> </DIV>
<DIV><BR><BR>--- On <B>Wed, 6/5/09, kyungchan chae <I><ckcumaa@umich.edu></I></B> wrote:<BR></DIV>
<BLOCKQUOTE style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: rgb(16,16,255) 2px solid"><BR>From: kyungchan chae <ckcumaa@umich.edu><BR>Subject: RE: [gmx-users] extending simulations<BR>To: "'Discussion list for GROMACS users'" <gmx-users@gromacs.org><BR>Date: Wednesday, 6 May, 2009, 8:02 PM<BR><BR>
<DIV class=plainMail>If you want to extend your simulation, simply use the 'append' command.<BR><BR>: mdrun -append yes -cpi state.cpt<BR><BR>Extending a simulation is quite simple. However, if your trajectory file is<BR>larger than 2GB, you are going to have a problem. I tested it a few weeks<BR>ago and found out that the 'append' option only worked when the size of<BR>trajectory file is smaller than 2GB. I reported this issue to Gromacs<BR>bugzilla(#315). Please check my bug report. I really hope to share<BR>information about this issue.<BR><BR><BR><BR>-----Original Message-----<BR>From: <A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-bounces@gromacs.org" ymailto="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</A> [mailto:<A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-bounces@gromacs.org" ymailto="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</A>]<BR>On Behalf Of Anna
Marabotti<BR>Sent: Wednesday, May 06, 2009 8:31 AM<BR>To: <A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>Subject: [gmx-users] extending simulations<BR><BR>Dear all,<BR>I'd need to have a clarification about how to extend a simulation made using<BR>GROMACS 4 that has been<BR>interrupted on a system due to walltime expiration. On the Wiki section I<BR>see:<BR>"A simulation that has completed is extended using tpbconv, mdrun and<BR>checkpoint files (.cpt). A simulation<BR>that has terminated, but not completed, due to e.g. the queue time ending,<BR>or better: the use of the -maxh<BR>option of mdrun, can be continued without tpbconv. First the number of steps<BR>or time has to be changed in the<BR>.tpr file, then the simulation is continued from the last checkpoint with<BR>mdrun. This will produce a binary<BR>identical simulation that will be the same as it a
continuous run was made.<BR>tpbconv -s previous.tpr -extend timetoextendby -o next.tpr<BR>mdrun -s next.tpr -cpi previous.cpt"<BR><BR>If I understand well, the procedure using tpbconv should be applied only if<BR>I have finished my previous run<BR>of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case I have<BR>to use tpbconv and then mdrun. On<BR>the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns, the only<BR>command I should provide is:<BR><BR>mdrun -s previous.tpr -cpi previous.cpt<BR><BR>without modifying the previous.tpr file.<BR>Could you please confirm me about this point?<BR>Many thanks and best regards<BR>Anna<BR><BR>______________________________________________<BR>Anna Marabotti, Ph.D.<BR>Laboratory of Bioinformatics and Computational Biology<BR>Institute of Food Science, CNR<BR>Via Roma 64<BR>83100 Avellino (Italy)<BR>Phone: +39 0825 299651<BR>Fax: +39 0825 781585<BR>Skype: annam1972<BR>E-mail: <A
href="http://in.mc948.mail.yahoo.com/mc/compose?to=amarabotti@isa.cnr.it" ymailto="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A><BR>Web page: <A href="http://bioinformatica.isa.cnr.it/anna/anna.htm" target=_blank>http://bioinformatica.isa.cnr.it/anna/anna.htm</A><BR>____________________________________________________<BR>"If you think you are too small to make a difference, try sleeping with a<BR>mosquito"<BR><BR>_______________________________________________<BR>gmx-users mailing list <A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests
to the list. Use the <BR>www interface or send it to <A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>..<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users..php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR><BR><BR><BR>_______________________________________________<BR>gmx-users mailing list <A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target=_blank>http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please search the archive at <A href="http://www.gromacs.org/search" target=_blank>http://www.gromacs.org/search</A> before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it
to <A href="http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-request@gromacs.org" ymailto="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target=_blank>http://www.gromacs.org/mailing_lists/users.php</A><BR></DIV></BLOCKQUOTE></td></tr></table><br>
<!--3--><hr size=1></hr> Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition * <a href="http://in.rd.yahoo.com/tagline_firefox_1/*http://downloads.yahoo.com/in/firefox/?fr=om_email_firefox"> Click here!</a>