[gmx-users] how to choose -beginfit for g_msd?
Shang-Te Danny Hsu
hsu at nmr.chem.uu.nl
Tue Apr 19 15:43:24 CEST 2005
I am trying to determine lateral diffusion coefficients of molecules in
lipid membranes using g_msd. The trajectory is 20 ns long and I'd like
to analyse the segment of 5-20 ns with 2.5 ns intervals for statistics.
The command used is as follows:
g_msd -f A.xtc -s A.tpr -n group.ndx -b 5000 -e 20000 -trestart 2500
-lateral Z (with varied -beginfit values)
I noticed that the output depends very much on the choice of -beginfit
(see examples below) and I wonder whether -beginfit is an absloute value
like -b and -e or it is a relative value with respect to the time point
defined by -b? I assume the later is the case because the diffusion
coefficients are zero when -beginfit (7.5 ns) is set to be half of the
length of trajectory segment (5-20 ns).
-beginfit 0
D[ A] 0.072 (+/- 0.122) 1e-5 cm^2/s
D[ B] 0.061 (+/- 0.096) 1e-5 cm^2/s
-beginfit 3000
D[ A] 0.052 (+/- 0.117) 1e-5 cm^2/s
D[ B] 0.045 (+/- 0.082) 1e-5 cm^2/s
-beginfit 5000
D[ A] 0.028 (+/- 0.040) 1e-5 cm^2/s
D[ B] 0.025 (+/- 0.004) 1e-5 cm^2/s
-beginfit 7500
D[ A] -0.000 (+/- 0.188) 1e-5 cm^2/s
D[ B] 0.007 (+/- 0.203) 1e-5 cm^2/s
If so, when the standard deviation derived with six restarting time
points is twice as large as the average value, how and when are we
confident that the simulation is long enough?
Any suggestion?
--
Shang-Te Danny HSU
Department of NMR Spectroscopy
Bijvoet Center for Biomolecular Research
Utrecht University
Padualaan 8, 3584 CH Utrecht, the Netherlands
phone: +31-30-2539931 | fax: +31-30-2537623
e-mail: hsu at nmr.chem.uu.nl
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