Hi Dallas,<div><br></div><div>Thanks! <br><br><div class="gmail_quote">On Wed, Sep 21, 2011 at 12:14 AM, Dallas Warren <span dir="ltr"><<a href="mailto:Dallas.Warren@monash.edu">Dallas.Warren@monash.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div lang="EN-US" link="blue" vlink="purple">
<div><div class="im">
<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 <u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
</div><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?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The –b –e and –beginfit –endfit are not consistent with each other.<span style="font-size:11.0pt;color:#1F497D"><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> </span></p></div></div></blockquote><div><br></div><div>OK, that was a miss. However, when I make the " -e 300000 ", even then the same error comes. Also, when I remove the -b or -e options [that is using default ones], the error remains: </div>
<div><br></div><div><font class="Apple-style-span" color="#ff0000">Not enough points for fitting (0).</font></div><div><font class="Apple-style-span" color="#ff0000">Can not determine the diffusion constant.</font></div><div>
<br></div><div> Can you please help in making an example that shows how to put -b -e -beginfit -endfit consistently? Say, I want to use all the frames in my trajectory. So, in this case, as I have 300ns [or 300,000ps] trajectory, lets put -b 0 & -e 300,000. Now, say, I want to do fitting from 100ns up to 300ns. So, I put: -beginfit 100000 & -endfit 300000:</div>
<div><br></div><div>In total:</div><div><br></div><div><div>g_msd -f noWAT_all_sys3_xray_1ns_300ns.dcd.xtc -s noWAT_sys3_xray.tpr -o msd.xvg -rmcomm -b 0 -e 300000 -beginfit 100000 -endfit 300000 -trestart 10 -lateral z </div>
</div><div><br></div><div>again, fails to calculate diffusion coefficient. </div><div><br></div><div>Please check and suggest further. </div><div><br></div><div>Many Thanks,</div><div>--- Lalit </div><div><br></div><div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div lang="EN-US" link="blue" vlink="purple"><div><p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Catch ya,<br>
<br>
Dr. Dallas Warren<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Medicinal Chemistry and Drug Action<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D">Monash Institute of Pharmaceutical Sciences</span><span style="font-size:10.0pt;color:#1F497D">, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<a href="mailto:dallas.warren@monash.edu" target="_blank">dallas.warren@monash.edu</a><u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;color:#1F497D"><a href="tel:%2B61%203%209903%209304" value="+61399039304" target="_blank">+61 3 9903 9304</a><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;color:#1F497D">
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:#1F497D"><u></u> <u></u></span></p>
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<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-size:10.0pt">From:</span></b><span style="font-size:10.0pt"> <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>]
<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<u></u><u></u></span></p>
</div>
</div><div><div></div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Hi All,<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">I am trying to use g_msd for a system of bilayer+protein+ions (water removed for convenience).<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<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. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><b>However when I use g_msd, like this:</b> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<div>
<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 <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><b>The output is like this:</b> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<div>
<p class="MsoNormal">Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Select a group to calculate mean squared displacement for:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 0 ( System) has 30044 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 1 ( Protein) has 2381 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 2 ( Protein-H) has 1204 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 3 ( C-alpha) has 144 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 4 ( Backbone) has 432 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 5 ( MainChain) has 575 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 6 ( MainChain+Cb) has 713 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 7 ( MainChain+H) has 575 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 8 ( SideChain) has 1806 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 9 ( SideChain-H) has 629 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 10 ( Prot-Masses) has 2381 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 11 ( non-Protein) has 27663 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 12 ( Ion) has 2 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 13 ( CAL) has 2 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 14 ( UNK) has 19600 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 15 ( SOP) has 7980 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 16 ( CLA) has 13 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 17 ( POT) has 68 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 18 ( Other) has 27661 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 19 ( CAL) has 2 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 20 ( UNK) has 19600 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 21 ( SOP) has 7980 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 22 ( CLA) has 13 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 23 ( POT) has 68 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Select a group: 0<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Selected 0: 'System'<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Now select a group for center of mass removal:<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 0 ( System) has 30044 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 1 ( Protein) has 2381 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 2 ( Protein-H) has 1204 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 3 ( C-alpha) has 144 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 4 ( Backbone) has 432 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 5 ( MainChain) has 575 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 6 ( MainChain+Cb) has 713 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 7 ( MainChain+H) has 575 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 8 ( SideChain) has 1806 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 9 ( SideChain-H) has 629 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 10 ( Prot-Masses) has 2381 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 11 ( non-Protein) has 27663 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 12 ( Ion) has 2 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 13 ( CAL) has 2 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 14 ( UNK) has 19600 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 15 ( SOP) has 7980 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 16 ( CLA) has 13 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 17 ( POT) has 68 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 18 ( Other) has 27661 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 19 ( CAL) has 2 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 20 ( UNK) has 19600 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 21 ( SOP) has 7980 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 22 ( CLA) has 13 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Group 23 ( POT) has 68 elements<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Select a group: 0<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Selected 0: 'System'<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">Reading frame 30000 time 0.000 <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Used 30003 restart points spaced 10 ps over 0 ps<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Fitting from 100000 to 300000 ps<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal"><b><span style="color:red">Not enough points for fitting (0).<br>
Can not determine the diffusion constant.</span></b><u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Back Off! I just backed up msd.xvg to ./#msd.xvg.17#<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">gcq#80: "Everybody Lie Down On the Floor and Keep Calm" (KLF)<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">********************************************************************************************************************************<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<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? <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<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.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Let me know if more information is needed. Please suggest and help. All help is truly appreciated. <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Many Thanks,<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">--- Lalit<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">p.s.: all relevant files can be obtained from: <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><a href="http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/" target="_blank">http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/</a> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal"> <u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div></div></div>
</div>
</div>
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