[gmx-users] how to choose -beginfit for g_msd?

[David van der Spoel]

On Tue, 2005-04-19 at 15:43 +0200, Shang-Te Danny Hsu wrote:
> 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).

Try without -beginfit. Check the figure, you can easily see how well it
is approximated by a straight line. You can also use xmgrace to fit a
line to it and check the correlation coefficient. 

> 
> -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?
> 
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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