[gmx-users] g_msd: Not enough points for fitting (0). Can not determine the diffusion constant
Lalit
upmunyu at gmail.com
Wed Sep 21 08:03:41 CEST 2011
Hi Dallas,
Thanks!
On Wed, Sep 21, 2011 at 12:14 AM, Dallas Warren <Dallas.Warren at monash.edu>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
> 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/ ****
>
> ** **
>
> ** **
>
> ****
>
> ** **
>
> --
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