[gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant

[Lalit]

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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