Hi All,<div><br></div><div>I am trying to use g_msd for a system of bilayer+protein+ions (water removed for convenience).</div><div><br></div><div>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.</div>
<div><br></div><div>Let me add that <u>g_density</u> works fine so I have reasons to believe that {.tpr} file is OK for these purposes. </div><div><br></div><div><b>However when I use g_msd, like this:</b> </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 30000 -beginfit 100000 -endfit 300000 -trestart 10 -lateral z </div><div><br></div></div><div><br></div>
<div><b>The output is like this:</b> </div><div><br></div><div><div>Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)</div><div>Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)</div><div>
<br></div><div>Select a group to calculate mean squared displacement for:</div><div>Group 0 ( System) has 30044 elements</div><div>Group 1 ( Protein) has 2381 elements</div><div>Group 2 ( Protein-H) has 1204 elements</div>
<div>Group 3 ( C-alpha) has 144 elements</div><div>Group 4 ( Backbone) has 432 elements</div><div>Group 5 ( MainChain) has 575 elements</div><div>Group 6 ( MainChain+Cb) has 713 elements</div>
<div>Group 7 ( MainChain+H) has 575 elements</div><div>Group 8 ( SideChain) has 1806 elements</div><div>Group 9 ( SideChain-H) has 629 elements</div><div>Group 10 ( Prot-Masses) has 2381 elements</div>
<div>Group 11 ( non-Protein) has 27663 elements</div><div>Group 12 ( Ion) has 2 elements</div><div>Group 13 ( CAL) has 2 elements</div><div>Group 14 ( UNK) has 19600 elements</div>
<div>Group 15 ( SOP) has 7980 elements</div><div>Group 16 ( CLA) has 13 elements</div><div>Group 17 ( POT) has 68 elements</div><div>Group 18 ( Other) has 27661 elements</div>
<div>Group 19 ( CAL) has 2 elements</div><div>Group 20 ( UNK) has 19600 elements</div><div>Group 21 ( SOP) has 7980 elements</div><div>Group 22 ( CLA) has 13 elements</div>
<div>Group 23 ( POT) has 68 elements</div><div>Select a group: 0</div><div>Selected 0: 'System'</div><div><br></div><div>Now select a group for center of mass removal:</div><div>Group 0 ( System) has 30044 elements</div>
<div>Group 1 ( Protein) has 2381 elements</div><div>Group 2 ( Protein-H) has 1204 elements</div><div>Group 3 ( C-alpha) has 144 elements</div><div>Group 4 ( Backbone) has 432 elements</div>
<div>Group 5 ( MainChain) has 575 elements</div><div>Group 6 ( MainChain+Cb) has 713 elements</div><div>Group 7 ( MainChain+H) has 575 elements</div><div>Group 8 ( SideChain) has 1806 elements</div>
<div>Group 9 ( SideChain-H) has 629 elements</div><div>Group 10 ( Prot-Masses) has 2381 elements</div><div>Group 11 ( non-Protein) has 27663 elements</div><div>Group 12 ( Ion) has 2 elements</div>
<div>Group 13 ( CAL) has 2 elements</div><div>Group 14 ( UNK) has 19600 elements</div><div>Group 15 ( SOP) has 7980 elements</div><div>Group 16 ( CLA) has 13 elements</div>
<div>Group 17 ( POT) has 68 elements</div><div>Group 18 ( Other) has 27661 elements</div><div>Group 19 ( CAL) has 2 elements</div><div>Group 20 ( UNK) has 19600 elements</div>
<div>Group 21 ( SOP) has 7980 elements</div><div>Group 22 ( CLA) has 13 elements</div><div>Group 23 ( POT) has 68 elements</div><div>Select a group: 0</div><div>Selected 0: 'System'</div>
<div>Reading frame 30000 time 0.000 </div><div><br></div><div>Used 30003 restart points spaced 10 ps over 0 ps</div><div><br></div><div>Fitting from 100000 to 300000 ps</div><div><br></div><b><font class="Apple-style-span" color="#ff0000">Not enough points for fitting (0).<br>
Can not determine the diffusion constant.</font></b><br><div><br></div><div>Back Off! I just backed up msd.xvg to ./#msd.xvg.17#</div><div><br></div><div>gcq#80: "Everybody Lie Down On the Floor and Keep Calm" (KLF)</div>
</div><div><br></div><div>********************************************************************************************************************************</div><div><br></div><div>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? </div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div><div><br></div>
<div>Let me know if more information is needed. Please suggest and help. All help is truly appreciated. </div><div><br></div><div>Many Thanks,</div><div>--- Lalit</div><div><br></div><div>p.s.: all relevant files can be obtained from: </div>
<div><br></div><div><a href="http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/">http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/</a> </div><div><br></div><div><br></div><div> </div><div><br></div>