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</o:shapelayout></xml><![endif]--></head><body lang=DA link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Hi Xavier,<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>That worked, thanks… Would it also work if I just gave the old state.cpt file to mdrun?<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Jesper<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] <b>On Behalf Of </b>XAvier Periole<br><b>Sent:</b> 24. februar 2011 12:19<br><b>To:</b> Discussion list for GROMACS users<br><b>Subject:</b> Re: [gmx-users] negative steps from tpbconv<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><p class=MsoNormal>Hi Jesper,<o:p></o:p></p><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>This occurs when you ask for a number of steps that exceed the <o:p></o:p></p></div><div><p class=MsoNormal>the size of an integer! I got the same problem recently ...<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>The only solution I found was to make a new mdp file where t0 <o:p></o:p></p></div><div><p class=MsoNormal>is the old time and asking for the extension you need ... you can<o:p></o:p></p></div><div><p class=MsoNormal>give trr and edr files to grompp so the tpr file is a continuation of <o:p></o:p></p></div><div><p class=MsoNormal>earlier one ...<o:p></o:p></p></div><div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>XAvier.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p><div><div><p class=MsoNormal>On Feb 24, 2011, at 11:50 AM, Jesper Sørensen wrote:<o:p></o:p></p></div><p class=MsoNormal><br><br><o:p></o:p></p><div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Hi,</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>I am trying to extend the run time in tpr file to include more steps using tpbconv…</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>This has worked well for a while, but now I get two errors…</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>One is that it writes “now -2074660000 steps”, which doesn’t make sense – why is this number negative…</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Also, “You've simulated long enough. Not writing tpr file”</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>If I extend the simulation using the –nsteps flag, then it will write the tpr file, but still comes up with negative numbers whens starting mdrun with the file, which mdrun does not exactly like.</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Output is a s follows:</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>READING COORDS, VELS AND BOX FROM TRAJECTORY ../T305/512DPPC_9728W_305K_625ns.trr...</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>trn version: GMX_trn_file (single precision)</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Read trr frame 4166: step 2124660000 time 53116500.000</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Using frame of step 2124660000 time 5.31165e+07</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Extending remaining runtime of by 625000 ps (now -2074660000 steps)</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>You've simulated long enough. Not writing tpr file</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'> </span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Best regards,</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'>Jesper</span><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:black'><o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:13.5pt;font-family:"Helvetica","sans-serif";color:black'>--<span class=apple-converted-space> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class=apple-converted-space> </span><a href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a><span class=apple-converted-space> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class=apple-converted-space> </span><br>www interface or send it to<span class=apple-converted-space> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class=apple-converted-space> </span><a href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a><o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p></div></div></div></body></html>