This is the normal behaviour for a MSD vs. time plot. Actually, as set
by default in g_msd, neither the first seconds nor the last ones are
taking into consideration to calculate the difussion constant.
The explanation for the non-liear curves might be the following. On one
hand, at the begining, the behavior is not brownian -- in some places it
is refered as "free-flight" or just as difussion at short times
(JCP,125,204703 is a good ref) -- On the other hand, as the average is
obtained by taking different starting times along the trajectory, there
would be much more points to average corresponding to the first seconds
of MSD, but for large times, just the few reference times corresponding
to the begining of the trajectory will contribute to the average and the
these final values turn to be not reliable.
So, the slope at the last 2 ns is not related to any physical event. You
should take the linear part corresponding to the middle of the time
range. Anyway, check if that region is large enough, if not you might
enlarge you simulation time (maybe 40-50ns).
Javier
El 07/10/10 18:36, tekle...@ualberta.ca escribió:
Dear Gromacs,
I have been calculating the self Diffusion constant of my system.
Surfactants in a different solvents of the same volume. After
simulation for 20ns I found the following data for the trajectory of
the mean square displacement.
# D[ TPA] = 0.2039 (+/- 0.0503) (1e-5 cm^2/s)
0 0
2 0.0105286
4 0.0162435
6 0.0212711
8 0.026031
10 0.0307584
12 0.035134
14 0.0393323
16 0.0434628
18 0.0475354
20 0.0516609
-
-
-
-
-
-
920 1.16467
922 1.16756
924 1.1703
926 1.17267
928 1.17383
930 1.17483
932 1.17581
934 1.17754
936 1.17957
938 1.18199
940 1.1829
942 1.18596
944 1.18871
946 1.19099
948 1.19219
950 1.19321
952 1.19445
954 1.19613
956 1.19838
-
-
-
-
-
-
10576 11.7747
10578 11.785
10580 11.7817
10582 11.7833
10584 11.7847
10586 11.784
10588 11.7855
10590 11.7904
10592 11.7926
10594 11.7943
10596 11.8036
10598 11.8141
10600 11.8112
-
-
-
-
-
-
19960 36.4106
19962 36.2607
19964 39.9243
19966 39.7493
19968 39.6744
19970 39.5838
19972 39.6723
19974 39.6374
19976 39.518
19978 39.4935
19980 39.3834
19982 39.1136
19984 42.3888
19986 42.168
19988 42.1337
19990 41.9395
19992 42.0065
19994 42.0993
19996 41.8652
19998 41.8419
20000 41.9419
20002 41.6049
From my data, the graph shows a linear trend until 18ns but as soon as
it reaches around 19, 20ns it dramatically increases the MSD value.
Since the surfactants form aggregation I was expecting the MSD curve
to go down. Is any explanation for that. Why? suddenly increases the
MSD curve. Which is then the correct slop then!
Thank you
Rob
--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
