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

[Dallas Warren]

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
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] 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/




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110921/e6abf3d8/attachment.html>