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<p class="MsoNormal">g_msd -f noWAT_all_sys3_xray_1ns_300ns.dcd.xtc -s noWAT_sys3_xray.tpr -o msd.xvg -rmcomm -b 0 -e 30000 -beginfit 100000 -endfit 300000 -trestart 10 -lateral z <o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">So the last frame you want it to read from the trajectory is at 30ns, but you want it to begin the fitting from 100ns?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The –b –e and –beginfit –endfit are not consistent with each other.<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:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Medicinal Chemistry and Drug Action<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
dallas.warren@monash.edu<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+61 3 9903 9304<br>
---------------------------------<br>
When the only tool you own is a hammer, every problem begins to resemble a nail.</span><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>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span 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>Lalit<br>
<b>Sent:</b> Wednesday, 21 September 2011 2:54 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> [gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi All,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I am trying to use g_msd for a system of bilayer+protein+ions (water removed for convenience).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">I have a {.dcd} file with say, 30000 frames. Each frame was written at 5000 steps (i.e., frame saved 10ps each ). Thus, whole trajectory corresponds to 300,000 ps (300ns). I got {.tpr} file from grompp using a {.top} file from topotools.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Let me add that <u>g_density</u> works fine so I have reasons to believe that {.tpr} file is OK for these purposes. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>However when I use g_msd, like this:</b> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">]$ g_msd -f noWAT_all_sys3_xray_1ns_300ns.dcd.xtc -s noWAT_sys3_xray.tpr -o msd.xvg -rmcomm -b 0 -e 30000 -beginfit 100000 -endfit 300000 -trestart 10 -lateral z <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b>The output is like this:</b> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)<o:p></o:p></p>
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<p class="MsoNormal">Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Select a group to calculate mean squared displacement for:<o:p></o:p></p>
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<p class="MsoNormal">Group 0 ( System) has 30044 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 1 ( Protein) has 2381 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 2 ( Protein-H) has 1204 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 3 ( C-alpha) has 144 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 4 ( Backbone) has 432 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 5 ( MainChain) has 575 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 6 ( MainChain+Cb) has 713 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 7 ( MainChain+H) has 575 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 8 ( SideChain) has 1806 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 9 ( SideChain-H) has 629 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 10 ( Prot-Masses) has 2381 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 11 ( non-Protein) has 27663 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 12 ( Ion) has 2 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 13 ( CAL) has 2 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 14 ( UNK) has 19600 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 15 ( SOP) has 7980 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 16 ( CLA) has 13 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 17 ( POT) has 68 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 18 ( Other) has 27661 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 19 ( CAL) has 2 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 20 ( UNK) has 19600 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 21 ( SOP) has 7980 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 22 ( CLA) has 13 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 23 ( POT) has 68 elements<o:p></o:p></p>
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<p class="MsoNormal">Select a group: 0<o:p></o:p></p>
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<p class="MsoNormal">Selected 0: 'System'<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Now select a group for center of mass removal:<o:p></o:p></p>
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<div>
<p class="MsoNormal">Group 0 ( System) has 30044 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 1 ( Protein) has 2381 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 2 ( Protein-H) has 1204 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 3 ( C-alpha) has 144 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 4 ( Backbone) has 432 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 5 ( MainChain) has 575 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 6 ( MainChain+Cb) has 713 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 7 ( MainChain+H) has 575 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 8 ( SideChain) has 1806 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 9 ( SideChain-H) has 629 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 10 ( Prot-Masses) has 2381 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 11 ( non-Protein) has 27663 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 12 ( Ion) has 2 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 13 ( CAL) has 2 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 14 ( UNK) has 19600 elements<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Group 15 ( SOP) has 7980 elements<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Group 16 ( CLA) has 13 elements<o:p></o:p></p>
</div>
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<p class="MsoNormal">Group 17 ( POT) has 68 elements<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Group 18 ( Other) has 27661 elements<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Group 19 ( CAL) has 2 elements<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Group 20 ( UNK) has 19600 elements<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Group 21 ( SOP) has 7980 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 22 ( CLA) has 13 elements<o:p></o:p></p>
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<p class="MsoNormal">Group 23 ( POT) has 68 elements<o:p></o:p></p>
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<p class="MsoNormal">Select a group: 0<o:p></o:p></p>
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<p class="MsoNormal">Selected 0: 'System'<o:p></o:p></p>
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<p class="MsoNormal">Reading frame 30000 time 0.000 <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Used 30003 restart points spaced 10 ps over 0 ps<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Fitting from 100000 to 300000 ps<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="color:red">Not enough points for fitting (0).<br>
Can not determine the diffusion constant.</span></b><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Back Off! I just backed up msd.xvg to ./#msd.xvg.17#<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">gcq#80: "Everybody Lie Down On the Floor and Keep Calm" (KLF)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">********************************************************************************************************************************<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">After reading/following the mailing-list postings and manual/hints through general search, I couldn't figure out any error in my command. Am I missing something obvious? <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">What I know that my trajectory file is 30000 frames long that constitutes up to 300,000ps run time. So, I understand that I can use -beginfit and -endfit values anything between 0 and 300,000. Also, -trestart could be 10 or 20 or 30 as
such.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Whether I use, {.dcd.xtc or .dcd} file, the result is same. I got the {.xtc} file from trjconv [trjconv -pbc mol -center -s xx.tpr -f xx.dcd -o newXX.dcd.xtc]. I am using 4.5.4 version.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Let me know if more information is needed. Please suggest and help. All help is truly appreciated. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Many Thanks,<o:p></o:p></p>
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<p class="MsoNormal">--- Lalit<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">p.s.: all relevant files can be obtained from: <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/">http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/</a> <o:p></o:p></p>
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