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. 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/
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