[gmx-users] Re: g_msd additional information

[dakoenig]

Hi Justin,

thank you so far. Now I got some more specific questions regarding g_msd
I got my trajectory from 0-30ns. So far it should to be "correct".

I was analyzing this trajectory with g_msd and the following command:

g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 15000
-endfit 16000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 15000
-endfit 17000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 15000
-endfit 18000 -o D_coeff
and so on

I observed an slight linear decreasing diffusion coefficient. The error bars
instead were increasing (starting at -beginfit 15000 -endfit 23000)
dramatically. Why do I observe such a behavior?
Is this the reason:
http://gromacs.5086.n6.nabble.com/MSD-and-self-diffusion-td4411869.html

In addition to that I analyzed the trajectory every 1 ns:
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 1000 -endfit
2000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 2000 -endfit
3000 -o D_coeff
g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0 -e 30000 -beginfit 3000 -endfit
4000 -o D_coeff

Here I observed extreme fluctuations starting at 25ns. The errors bars
starting at 27ns were huge. Why do I observe these extreme error bars and
fluctuation for the last 3/5 ns?

I checked my whole trajectory (g_msd -f mdrun.xtc -s mdrun.tpr -nice 0 -b 0
-e 30000) as well, but it is a straight line, without any observable curves.

Thank you for your comments and help.

Daniel



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