<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><DIV><BR>Dear Sir:</DIV>
<DIV> I want to know version of groamcs and orca in your the qm/mm calculation? are they in parallel ?</DIV>
<DIV>thank you!</DIV>
<DIV><BR> <BR><BR><A class=plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR><BR>--- <B>11å¹´11月10日，周四, Micha Ben Achim Kunze <I><ucbtmbk@live.ucl.ac.uk></I></B> 写é“：<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>å‘件人: Micha Ben Achim Kunze <ucbtmbk@live.ucl.ac.uk><BR>主题: Re: [gmx-users] orca question and LA<BR>收件人: gmx-users@gromacs.org<BR>日期: 2011å¹´11月10æ—¥,周四,下åˆ7:35<BR><BR>
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<DIV>I hope you mean ./configure --with-qmmm-orca --without-qmmm-gaussian etc. <BR><BR><A class=yiv1296686137moz-txt-link-freetext href="http://wwwuser.gwdg.de/~ggroenh/qmmm.html" rel=nofollow target=_blank>http://wwwuser.gwdg.de/%7Eggroenh/qmmm.html</A> <BR><A class=yiv1296686137moz-txt-link-freetext href="http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html" rel=nofollow target=_blank>http://www.dddc.ac.cn/embo04/practicals/qmmm/qmmmvacuum.html</A><BR><A class=yiv1296686137moz-txt-link-abbreviated href="http://www.google.com/" rel=nofollow target=_blank>www.google.com</A><BR>etc.<BR><BR>For MPI, I can't really say as I did not get qm/mm with orca/gmx to run in parallel yet (using cp2k atm). Maybe someone else can advise you.<BR><BR>Cheers,<BR>Micha<BR><BR><BR>On 10/11/11 10:49, xi zhao wrote:
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<DIV>I install gmx : ./configure --without-qmmm-orca --without-qmmm-gaussian --enable-mpi</DIV>
<DIV><FONT style="BACKGROUND-COLOR: #c7edcc"> then make </FONT></DIV>
<DIV><FONT style="BACKGROUND-COLOR: #c7edcc"> make install </FONT></DIV>
<DIV><FONT style="BACKGROUND-COLOR: #c7edcc">are it right?</FONT></DIV>
<DIV><BR><BR><BR><A class=yiv1296686137plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=yiv1296686137pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A><BR><BR>--- <B>11å¹´11月10日，周四, Micha Ben Achim Kunze <I><A class=yiv1296686137moz-txt-link-rfc2396E href="http://cn.mc151.mail.yahoo.com/mc/compose?to=ucbtmbk@live.ucl.ac.uk" rel=nofollow target=_blank ymailto="mailto:ucbtmbk@live.ucl.ac.uk"><ucbtmbk@live.ucl.ac.uk></A></I></B> 写é“：<BR></DIV>
<BLOCKQUOTE style="BORDER-LEFT: rgb(16,16,255) 2px solid; PADDING-LEFT: 5px; MARGIN-LEFT: 5px"><BR>å‘件人: Micha Ben Achim Kunze <A class=yiv1296686137moz-txt-link-rfc2396E href="http://cn.mc151.mail.yahoo.com/mc/compose?to=ucbtmbk@live.ucl.ac.uk" rel=nofollow target=_blank ymailto="mailto:ucbtmbk@live.ucl.ac.uk"><ucbtmbk@live.ucl.ac.uk></A><BR>主题: Re: [gmx-users] orca question and LA<BR>收件人: <A class=yiv1296686137moz-txt-link-abbreviated href="http://cn.mc151.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org" rel=nofollow target=_blank ymailto="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR>日期: 2011å¹´11月10æ—¥,周四,下åˆ4:47<BR><BR>
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<DIV>Hey there,<BR><BR>my last mail got stuck as it was a bit too large it seems. As I wrote earlier there should be NO coordinates in the infofile... It looks like you have a problem with gmx not preparing a correct .inp file which should include keywords from the infofile, the coordinates of the QMsubsystem and pointcharges (depending on the method you use). Are you sure everything is compiled correct and that you specified your virtual atoms correctly for your force field (and with correct positions/constrains)? Have a look if gmx actually creates an .inp file and if yes what it includes.<BR><BR>Again, you should go through Gerrit's tutorials, they should get you going. There are also instructions on how to set up LAs for different force fields.<BR><BR>Cheers,<BR>Micha<BR>On 10/11/11 01:19, xi zhao wrote:
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<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman">Dear Sir:</FONT></SPAN> </DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3><FONT face="Times New Roman"><SPAN> </SPAN>How to write a correct BASENAME.ORCAINFO file? According to the <SPAN style="COLOR: black">instruction “</SPAN>In the ORCAINFO-file the method, basis set and all other ORCA-specific keywords must be given.†It means that BASENAME.ORCAINFO may not contain coordinates of QMatoms part, but when groamcs-ORCA runs , it has errors: Calling '/home/user/orca_x86_64_exe_r2131/orca pyp_qm.inp >> pyp_qm.out'</FONT></FONT></SPAN> </DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman">No atoms to convert in Cartesian2Internal" ; </FONT></SPAN></DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman">When BASENAME.ORCAINFO has coordinates of QMatoms part, ORCA cannot recognizes the LA (gromacs dummy atom) in the QMatoms , how to deal with LA , delete LA in the BASENAME.ORCAINFO? In fact, the stand-alone version of Orca can normally calculates it. Of course, LA must modified!</FONT></SPAN> </DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman"> </FONT></SPAN> </DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman">Kind regards!</FONT></SPAN> </DIV>
<P style="MARGIN: 0cm 0cm 0pt" class=yiv1296686137MsoNormal><SPAN lang=EN-US><FONT size=3 face="Times New Roman"> </FONT></SPAN><BR><BR><A class=yiv1296686137plink href="http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844" rel=nofollow target=_blank><IMG class=yiv1296686137pimg border=0 alt=4 src="http://opi.yahoo.com/online?u=zhaoxiitc2002&t=4&l=cn"></A></DIV></TD></TR></TBODY></TABLE><BR>
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