<br /><br /><span>On 01/24/11, <b class="name">Mark Abraham </b> <mark.abraham@anu.edu.au> wrote:</span><blockquote cite="mid: <27673_1295829232_4D3CC8ED_27673_49671_1_769085bf7d9.4d3d6360@anu.edu.au" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><br /><br /><span>On 01/24/11, <b class="name">Luca Bellucci </b> <luca.bellucci_s3@unimore.it> wrote:</span><blockquote cite="mid:99f027e7083262a58d233fe5b8f9d8b3.squirrel@webmail2.unimore.it" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain">hanks Mark for quick replay.<br />it is 4.5.3<br />This is the log file at restart point.<br /><br />-----------------------------------------------------------<br />Restarting from checkpoint, appending to previous log file.<br /><br />Log file opened on Sun Jan 23 23:40:07 2011<br />Host: ionode8 pid: 2916 nodeid: 0 nnodes: 64<br />The Gromacs distribution was built Thu Nov 18 14:35:49 CET 2010 by<br />cin0644a@loginfn (Linux 2.6.16.60-0.42.10-ppc64 ppc64)<br />[..]<br />Initializing Replica Exchange<br />Repl There are 64 replicas:<br />Multi-checking the number of atoms ... OK<br />Multi-checking the integrator ... OK<br />Multi-checking init_step+nsteps ... OK<br />Multi-checking first exchange step: init_step/-replex ... OK<br />Multi-checking the temperature coupling ... OK<br />Multi-checking the number of temperature coupling groups ... OK<br />Multi-checking the pressure coupling ... OK<br />Multi-checking free energy ... OK<br />[..]</div></blockquote><br />Seeing the whole logfile up to the first energy output would be more helpful.</div></blockquote><br />Also, stderr and stdout can have useful diagnostic information here.<br /><br />Mark<br /><br /><blockquote cite="mid: <27673_1295829232_4D3CC8ED_27673_49671_1_769085bf7d9.4d3d6360@anu.edu.au" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text html"><br /><br />Mark<br /><br /><blockquote cite="mid:99f027e7083262a58d233fe5b8f9d8b3.squirrel@webmail2.unimore.it" class="iwcQuote" style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0pt;" type="cite"><div class="mimepart text plain"><br />Started mdrun on node 0 Sun Jan 23 23:40:07 2011<br /><br /><br />> On 24/01/2011 8:57 AM, Luca Bellucci wrote:<br />> > Dear all,<br />> > I known that in repl_ex.c is implemented the<br />> > H-REMD. It seems to work, however<br />> > H-REMD is not documented, thus I am testing it.<br />> > I performed a test in a BlueGene cluster:<br />> ><br />> > mpirun -mode VN -np 4096 mdrun_mpi_bg -s md.tpr -np 16 -multi 128<br />> > -replex 2000<br />> ><br />> > it works fine.<br />> ><br />> > I restarted with this command:<br />> ><br />> > mpirun -mode VN -np 4096 mdrun_mpi_bg -s md.tpr -cpi state.cpt -append<br />> > -np 16 -multi 128 -replex 2000<br />> ><br />> > I followed the GROMACS "Doing Restarts" section, however it does not<br />> > work as expected; the trajecory and energy files are reinitialized and I<br />> > lost most of the MD informations.<br />> > Only log files were updated as expected.<br />><br />> Is this with the latest GROMACS version? If not, please try that.<br />><br />> Mark<br /><br />-- <br />gmx-developers mailing list<br />gmx-developers@gromacs.org<br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="1">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br />Please don't post (un)subscribe requests to the list. Use the <br />www interface or send it to gmx-developers-request@gromacs.org.<br /></div></blockquote>
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