On 3/28/13 5:32 PM, Ahmet yıldırım wrote:
Please see plot:
http://imageshack.us/photo/my-images/35/diffusion.png/
How did you come up with your "expected" values? What does the original msd.xvg
plot look like? It should be basically linear. If it's not, then you have
found the source of your problem.
-Justin
2013/3/28 Justin Lemkul <jalem...@vt.edu>
On Thu, Mar 28, 2013 at 9:59 AM, Ahmet yıldırım <ahmedo...@gmail.com>
wrote:
Dear users,
Again, I have strange results (for 10,50,100,150,200 ns). I am wondering,
is there a bug with g_msd?
I see no evidence for a bug, and you should avoid such speculation unless
you know exactly how the program should behave. Only then, after an
analysis of known quantities or behavior, can we discuss bugginess. Do you
know how g_msd works? Do you know what all of the flags are doing, or are
you just making adjustments hoping for clarity? You may find the following
post very illuminating:
http://lists.gromacs.org/pipermail/gmx-users/2010-July/052512.html
-Justin
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 <vvcha...@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 <sp...@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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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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