Hi Dallas, Thanks!
On Wed, Sep 21, 2011 at 12:14 AM, Dallas Warren <[email protected]>wrote: > 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 **** > > ** ** > > 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?**** > > ** ** > > The –b –e and –beginfit –endfit are not consistent with each other.**** > > ** > 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: Not enough points for fitting (0). Can not determine the diffusion constant. 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: In total: 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 again, fails to calculate diffusion coefficient. Please check and suggest further. Many Thanks, --- Lalit > ** > > Catch ya, > > Dr. Dallas Warren**** > > Medicinal Chemistry and Drug Action**** > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > [email protected]**** > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. **** > > ** ** > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Lalit > *Sent:* Wednesday, 21 September 2011 2:54 PM > *To:* Discussion list for GROMACS users > *Subject:* [gmx-users] g_msd: Not enough points for fitting (0). Can not > determine the diffusion constant**** > > ** ** > > Hi All,**** > > ** ** > > I am trying to use g_msd for a system of bilayer+protein+ions (water > removed for convenience).**** > > ** ** > > 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.**** > > ** ** > > Let me add that *g_density* works fine so I have reasons to believe that > {.tpr} file is OK for these purposes. **** > > ** ** > > *However when I use g_msd, like this:* **** > > ** ** > > ]$ 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 **** > > ** ** > > ** ** > > *The output is like this:* **** > > ** ** > > Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)**** > > Reading file noWAT_sys3_xray.tpr, VERSION 4.5.4 (single precision)**** > > ** ** > > Select a group to calculate mean squared displacement for:**** > > Group 0 ( System) has 30044 elements**** > > Group 1 ( Protein) has 2381 elements**** > > Group 2 ( Protein-H) has 1204 elements**** > > Group 3 ( C-alpha) has 144 elements**** > > Group 4 ( Backbone) has 432 elements**** > > Group 5 ( MainChain) has 575 elements**** > > Group 6 ( MainChain+Cb) has 713 elements**** > > Group 7 ( MainChain+H) has 575 elements**** > > Group 8 ( SideChain) has 1806 elements**** > > Group 9 ( SideChain-H) has 629 elements**** > > Group 10 ( Prot-Masses) has 2381 elements**** > > Group 11 ( non-Protein) has 27663 elements**** > > Group 12 ( Ion) has 2 elements**** > > Group 13 ( CAL) has 2 elements**** > > Group 14 ( UNK) has 19600 elements**** > > Group 15 ( SOP) has 7980 elements**** > > Group 16 ( CLA) has 13 elements**** > > Group 17 ( POT) has 68 elements**** > > Group 18 ( Other) has 27661 elements**** > > Group 19 ( CAL) has 2 elements**** > > Group 20 ( UNK) has 19600 elements**** > > Group 21 ( SOP) has 7980 elements**** > > Group 22 ( CLA) has 13 elements**** > > Group 23 ( POT) has 68 elements**** > > Select a group: 0**** > > Selected 0: 'System'**** > > ** ** > > Now select a group for center of mass removal:**** > > Group 0 ( System) has 30044 elements**** > > Group 1 ( Protein) has 2381 elements**** > > Group 2 ( Protein-H) has 1204 elements**** > > Group 3 ( C-alpha) has 144 elements**** > > Group 4 ( Backbone) has 432 elements**** > > Group 5 ( MainChain) has 575 elements**** > > Group 6 ( MainChain+Cb) has 713 elements**** > > Group 7 ( MainChain+H) has 575 elements**** > > Group 8 ( SideChain) has 1806 elements**** > > Group 9 ( SideChain-H) has 629 elements**** > > Group 10 ( Prot-Masses) has 2381 elements**** > > Group 11 ( non-Protein) has 27663 elements**** > > Group 12 ( Ion) has 2 elements**** > > Group 13 ( CAL) has 2 elements**** > > Group 14 ( UNK) has 19600 elements**** > > Group 15 ( SOP) has 7980 elements**** > > Group 16 ( CLA) has 13 elements**** > > Group 17 ( POT) has 68 elements**** > > Group 18 ( Other) has 27661 elements**** > > Group 19 ( CAL) has 2 elements**** > > Group 20 ( UNK) has 19600 elements**** > > Group 21 ( SOP) has 7980 elements**** > > Group 22 ( CLA) has 13 elements**** > > Group 23 ( POT) has 68 elements**** > > Select a group: 0**** > > Selected 0: 'System'**** > > Reading frame 30000 time 0.000 **** > > ** ** > > Used 30003 restart points spaced 10 ps over 0 ps**** > > ** ** > > Fitting from 100000 to 300000 ps**** > > ** ** > > *Not enough points for fitting (0). > Can not determine the diffusion constant.***** > > ** ** > > Back Off! I just backed up msd.xvg to ./#msd.xvg.17#**** > > ** ** > > gcq#80: "Everybody Lie Down On the Floor and Keep Calm" (KLF)**** > > ** ** > > > ******************************************************************************************************************************** > **** > > ** ** > > 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? **** > > ** ** > > 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.**** > > ** ** > > 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.**** > > ** ** > > Let me know if more information is needed. Please suggest and help. All > help is truly appreciated. **** > > ** ** > > Many Thanks,**** > > --- Lalit**** > > ** ** > > p.s.: all relevant files can be obtained from: **** > > ** ** > > http://lalitpkc.phy.uic.edu/~lalit/GROMACS_files/ **** > > ** ** > > ** ** > > **** > > ** ** > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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