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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Roland,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for the reply! Looks like the error messages were generated by Cuda6.0 (see errors below) instead of GROMACS. Switching back to ICC13.1 and turning off static-libraries worked for us.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Kevin<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>=====================================================================================================================================<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>“In file included from /opt/apps/cuda/6.0/include/cuda_runtime.h(59),<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>/opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error: #error directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> #error -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> ^<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>/opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error: #error directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> #error -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> ^<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> from /admin/build/admin/rpms/stampede/BUILD/gromacs-5.0.1/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu(0):<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>/opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error: #error directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> #error -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> ^<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>In file included from /opt/apps/cuda/6.0/include/cuda_runtime.h(59),<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'> from /admin/build/admin/rpms/stampede/BUILD/gromacs-5.0.1/src/gromacs/gmxlib/cuda_tools/pmalloc_cuda.cu(0):<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>/opt/apps/cuda/6.0/include/host_config.h(72): catastrophic error: #error directive: -- unsupported ICC configuration! Only ICC 13.1 on Linux x86_64 is supported!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>“<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><a name="_MailEndCompose"><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></a></p><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> gromacs.org_gmx-developers-bounces@maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se] <b>On Behalf Of </b>Roland Schulz<br><b>Sent:</b> Monday, September 29, 2014 11:16 AM<br><b>To:</b> gmx-developers@gromacs.org<br><b>Subject:</b> Re: [gmx-developers] ICC 14 support<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>what problem do you have with ICC14? Both ICC14 and ICC15 should work fine. There was an issue with ICC14+static-libraries (9e8061e13f48, 4.6.7 and 5.0.1) and ICC14+unit-tests(b0e60e91add6, 5.0.1). Both are fixed in release-5-0 and will be included 5.0.2. You can either use the release-5-0 branch, just apply the patch, wait till 5.0.2 (should be soon), or don't use static-libraries (default) and don't try to run the unit-tests (the compiler issue isn't present in the main code thus even though the unit tests fail the actual program is OK).<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Roland<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On Mon, Sep 29, 2014 at 10:35 AM, Kevin Chen <<a href="mailto:fch6699@gmail.com" target="_blank">fch6699@gmail.com</a>> wrote:<o:p></o:p></p><blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in'><p class=MsoNormal>Hi Guys,<br><br>Was wondering if GROMACS will support ICC 14 in the near future?<br><br>Kevin Chen, Ph.D.<br>HPC Applications, TACC<br><br><br>-----Original Message-----<br>From: <a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a> [mailto:<a href="mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se">gromacs.org_gmx-developers-bounces@maillist.sys.kth.se</a>] On Behalf Of Alexey Shvetsov<br>Sent: Sunday, September 28, 2014 3:09 PM<br>To: <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>Subject: Re: [gmx-developers] Possible bug in gmx<br><br>Mark Abraham писал 28-09-2014 18:17:<br>> How about a redmine issue - this thread's not about GROMACS<br>> development, per se ;-)<br><br>Sorry about that =D<br><br>Redmine issue <a href="http://redmine.gromacs.org/issues/1607" target="_blank">http://redmine.gromacs.org/issues/1607</a><br>With relevant tpr file attached<br>><br>> Mark<br>><br>> On Sun, Sep 28, 2014 at 3:18 PM, Alexey Shvetsov<br>> <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>><br>>> Hi Berk!<br>>><br>>> Its not a cut and paste error, also there are no pdb dumps.<br>>> Also I see this error before with other systems.<br>>><br>>> I can provide tpr file for that system<br>>><br>>> <a href="https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr" target="_blank">https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr</a> [1]<br>>><br>>> Berk Hess писал 28-09-2014 16:37:<br>>><br>>> Hi,<br>>><br>>> I assume that your old and be coordinates being identical is correct<br>>> and not a cut-and-paste error.<br>>> This seems a bit strange or do you freeze part of the system?<br>>> The only things moving here are then the domain boundaries and I<br>>> don't see an issue there, since they only moved a little.<br>>><br>>> Do you have any more output besides the error message? PDB dump files<br>>> maybe?<br>>><br>>> Cheers,<br>>><br>>> Berk<br>>><br>>> On 09/28/2014 02:22 PM, Alexey Shvetsov wrote:<br>>> Hi,<br>>><br>>> just wanna add that this error seems to be reproducable even on<br>>> single node. Also i get same error for gpu runs.<br>>> However i dont see it in large systems (800k+ atoms) running on large<br>>> number of cpus (512+)<br>>><br>>> Alexey Shvetsov писал 28-09-2014 13:44:<br>>> Hi,<br>>><br>>> DD grid is<br>>><br>>> Domain decomposition grid 4 x 1 x 1, separate PME ranks 0 PME domain<br>>> decomposition: 4 x 1 x 1<br>>><br>>> for 4 node setup<br>>><br>>> and<br>>><br>>> Domain decomposition grid 4 x 2 x 1, separate PME ranks 0 PME domain<br>>> decomposition: 4 x 2 x 1<br>>><br>>> for 8 node setup<br>>><br>>> It's reproducable with 5.0 release and latest git master. I try to<br>>> check if its reproducable with 1 node. Also i can provide tpr file<br>>> for this system<br>>><br>>> Mark Abraham писал 28-09-2014 13:28:<br>>> Hi,<br>>><br>>> It's hard to say on that information. There were some issues fixed in<br>>> the lead-up to GROMACS 5 with DD not always working with 2 domains in<br>>> a direction, but that's a pure guess. I'd assume you can reproduce<br>>> this with release-5-0 branch. Do you observe it with a single domain?<br>>> If not, then it's surely a bug (and should be submitted to redmine).<br>>><br>>> Mark<br>>><br>>> On Sun, Sep 28, 2014 at 11:18 AM, Alexey Shvetsov<br>>> <<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a>> wrote:<br>>><br>>> Hi all!<br>>><br>>> I'm doing some tests with small peptide and constantly getting this<br>>> error.<br>>> I get it with few systems.<br>>><br>>> Systems sizes are around 10k or 20k<br>>> I run it on 4 or 8 old nodes each with two xeon 54xx series<br>>><br>>> starting mdrun '2ZCH_3 in water'<br>>> 50000000 steps, 100000.0 ps (continuing from step 1881000, 3762.0<br>>> ps).<br>>><br>>> Step 13514000:<br>>> The charge group starting at atom 6608 moved more than the distance<br>>> allowed by the domain decomposition (1.112924) in direction X<br>>> distance out of cell -1.193103 Old coordinates: 5.467 0.298 3.636 New<br>>> coordinates: 5.467 0.298 3.636 Old cell boundaries in direction X:<br>>> 4.037 5.382 New cell boundaries in direction X: 4.089 5.452<br>>><br>>><br>> ----------------------------------------------------------------------<br>> ----<br>>> MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD with<br>>> errorcode 1.<br>>><br>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.<br>>> You may or may not see output from other processes, depending on<br>>> exactly when Open MPI kills them.<br>>><br>>><br>> ----------------------------------------------------------------------<br>> ----<br>>><br>>> -------------------------------------------------------<br>>> Program mdrun_mpi, VERSION 5.1-dev-20140922-20c00a9-dirty-unknown<br>>> Source code file:<br>>><br>>><br>> /var/tmp/alexxy/portage/sci-chemistry/gromacs-9999/work/gromacs-9999/s<br>> rc/gromacs/mdlib/domdec.cpp,<br>>> line: 4388<br>>><br>>> Fatal error:<br>>> A charge group moved too far between two domain decomposition steps<br>>> This usually means that your system is not well equilibrated For more<br>>> information and tips for troubleshooting, please check the GROMACS<br>>> website at <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a> [2] [1]<br>>> -------------------------------------------------------<br>>><br>>> -- Best Regards,<br>>> Alexey 'Alexxy' Shvetsov, PhD<br>>> Department of Molecular and Radiation Biophysics FSBI Petersburg<br>>> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,<br>>> Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>>> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>>> -- Gromacs Developers mailing list<br>>><br>>> * Please search the archive at<br>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a><br>>> [3] [2]<br>>> before posting!<br>>><br>>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a> [4]<br>>> [3]<br>>><br>>> * For (un)subscribe requests visit<br>>><br>>><br>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer</a><br>> s<br>>> [5]<br>>> [4] or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>>><br>>> Links:<br>>> ------<br>>> [1] <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a> [2] [2]<br>>> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> [3]<br>>> [3] <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a> [4] [4]<br>>><br>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer</a><br>> s<br>>> [5]<br>><br>> -- Best Regards,<br>> Alexey 'Alexxy' Shvetsov, PhD<br>> Department of Molecular and Radiation Biophysics FSBI Petersburg<br>> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,<br>> Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>><br>> --<br>> Best Regards,<br>> Alexey 'Alexxy' Shvetsov, PhD<br>> Department of Molecular and Radiation Biophysics FSBI Petersburg<br>> Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region,<br>> Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a><br>> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>> --<br>> Gromacs Developers mailing list<br>><br>> * Please search the archive at<br>> <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> [3]<br>> before posting!<br>><br>> * Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a> [4]<br>><br>> * For (un)subscribe requests visit<br>><br>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer</a><br>> s [5] or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>><br>><br>> Links:<br>> ------<br>> [1] <a href="https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr" target="_blank">https://biod.pnpi.spb.ru/~alexxy/gmx/psa_pep_ctrl.md_npt.tpr</a><br>> [2] <a href="http://www.gromacs.org/Documentation/Errors" target="_blank">http://www.gromacs.org/Documentation/Errors</a><br>> [3] <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a><br>> [4] <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>> [5]<br>> <a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developer</a><br>> s<br><br>--<br>Best Regards,<br>Alexey 'Alexxy' Shvetsov, PhD<br>Department of Molecular and Radiation Biophysics FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Leningrad region, Gatchina, Russia mailto:<a href="mailto:alexxyum@gmail.com">alexxyum@gmail.com</a> mailto:<a href="mailto:alexxy@omrb.pnpi.spb.ru">alexxy@omrb.pnpi.spb.ru</a><br>--<br>Gromacs Developers mailing list<br><br>* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!<br><br>* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br><br>* For (un)subscribe requests visit<br><a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br><span style='color:#888888'><br><span class=hoenzb>--</span><br><span class=hoenzb>Gromacs Developers mailing list</span><br><br><span class=hoenzb>* Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_List</a> before posting!</span><br><br><span class=hoenzb>* Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a></span><br><br><span class=hoenzb>* For (un)subscribe requests visit</span><br><span class=hoenzb><a href="https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers" target="_blank">https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers</a> or send a mail to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.</span></span><o:p></o:p></p></blockquote></div><p class=MsoNormal><br><br clear=all><o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309 <o:p></o:p></p></div></div></body></html>