[gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

Dear users,

This time, I calculated the diffusion coefficients of protein for each 10
ns of the simulation providing a total simulation time of 200 ns.
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 20 -beginfit -1
-endfit -1 -b 0 -e 10000
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 20 -beginfit -1
-endfit -1 -b 10001 -e 20000
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
-endfit -1 -b 20001 -e 30000
....
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
-endfit -1 -b 190001 -e 200000

I have strange Diffusion results (especially 10,50,100,150,200 ns). How can
I fix this problem?
Results:
Time (ns) D(cm^2/s)
10 0.1616
20 0.0735
30 0.0775
40 0.1097
50 0.1471
60 0.0468
70 0.0667
80 0.0727
90 0.0664
100 0.1336
110 0.0899
120 0.0572
130 0.0506
140 0.0723
150 0.1466
160 0.0703
170 0.081
180 0.0278
190 0.1121
200 0.3136



2013/3/27 Ahmet yıldırım <ahmedo047 at gmail.com>
>
> Dear users,
>
> I used the following commands to get diffusion constants (every 10 ns) of
a simulation of 100 ns . The number of frame is 5001 (write .xtc trajectory
every 20 ps).  I looked at RMSD vs average structure, RMSD vs starting
structure, Radius of gyration, RMSD matrix. This simulation has reached to
converge at last 50 ns.
> g_msd -f traj.xtc -s topol.tpr -o msd_1.xvg -b 0 -e 10000
> g_msd -f traj.xtc -s topol.tpr -o msd_2.xvg -b 10000 -e 20000
> g_msd -f traj.xtc -s topol.tpr -o msd_3.xvg -b 20000 -e 30000
> ...
> g_msd -f traj.xtc -s topol.tpr -o msd_10.xvg -b 90000 -e 100000
>
> 1.) I used the above commands without the following flags ( -type,
-lateral and -ten). Which diffusion will the above comands give? is it bulk
diffusion?
> Gromacs manual:
> -type:Compute diffusion coefficient in one direction:no, x, y or z
> -lateral:Calculate the lateral diffusion in a plane perpendicular to: no,
x, y or z
> -ten:Calculate the full tensor
> 2.) I plotted diffusions (10 values) as function of time. Diffusions dont
converge. Did I do any steps by mistake?
> 3.) From manual:
> The diffusion constant is calculated by least squares fitting a straight
line (D*t + c)...
> What is (D*t + c)? What are the meaning of D and c?
> 4.) What should be "Time between restarting points in trajectory"?
>
> Thanks in advance
> --
> Ahmet Yıldırım




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Ahmet Yıldırım