[gmx-users] Re: diffusion constant level off

[Ahmet yıldırım]

Dear users,

Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?

Commands for trestart to 20 ps:
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 10000 -e 20000
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 20 -beginfit -1
-endfit -1 -b 20000 -e 30000
...
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 20 -beginfit -1
-endfit -1 -b 190000 -e 200000

Commands for trestart to 1000 ps:
g_msd -f traj.xtc -s topol.top -o msd1.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 0 -e 10000
g_msd -f traj.xtc -s topol.top -o msd2.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 10000 -e 20000
g_msd -f traj.xtc -s topol.top -o msd3.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 20000 -e 30000
...
g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 1000 -beginfit -1
-endfit -1 -b 190000 -e 200000


D1 (cm^2/s):Diffusion for trestart to 20 ps
D2 (cm^2/s):Diffusion for trestart to 1000 ps
Time (ns) D1 D2
10 0.1616 0.1091
20 0.0735 0.0679
30 0.0775 0.0705
40 0.1097 0.1189
50 0.1471 0.1436
60 0.0468 0.048
70 0.0667 0.0652
80 0.0727 0.086
90 0.0664 0.0707
100 0.1336 0.114
110 0.0899 0.0841
120 0.0572 0.0598
130 0.0506 0.0482
140 0.0723 0.0767
150 0.1466 0.1439
160 0.0703 0.0601
170 0.081 0.0853
180 0.0278 0.027
190 0.1121 0.1024
200 0.3136 0.2981


2013/3/28 Dr. Vitaly Chaban <vvchaban at gmail.com>
>
> >
> > if I do as you said, I will get only one diffusion coefficient. I want
to
> > calculate one diffusion coefficient for each 10
> > ns of the simulation time of 200 ns. That is, I want to get 20 diffusion
> > values.
> >
> > 2013/3/28 David van der Spoel <spoel at xray.bmc.uu.se>
> >
> >> On 2013-03-28 10:40, Ahmet yıldırım wrote:
> >>
> >>> 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
> >>>
> >>
> >> Set trestart to 10001 (no restarts), or do one run with
> >>
> >> g_msd -f traj.xtc -s topol.top -o msd20.xvg -trestart 10000
> >>
>
>
> I believe the advice was to increase "trestart" and you can decide
> yourself how much to increase.
>
> Most likely, your protein deserves better sampling than 10 ns for a
> linear diffusion.
>
> Dr. Vitaly Chaban
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Ahmet Yıldırım