On 9/12/2011 5:37 AM, Sławomir Stachura wrote:
Hi!
Thanks Mark for reply. When I calculated fractional diffusion constant from
mass weighted MSD of long simulation I get sth about 0.05. But when I do the
same for centre of mass, considering that MSD is expressed in nm^2, the result
is 1.35. When I look into xvg file MSD of centre of mass is 10-20 times than
for mass-weighted (which is substantially wrong). So assuming that, by any
chance, centre of mass MSD is in A^2, calculated fractional diffusion constant
is of 0.02 magnitude, which is theoretically more understandable.
What I can show you is a sample of two MSDs:
- Mass weighted:
0 0
15 0.0150352
30 0.0198877
45 0.0235849
60 0.0267214
75 0.0294651
90 0.0319853
105 0.0342538
120 0.0364239
135 0.0384275
150 0.0403661
165 0.0421938
180 0.0439495
195 0.0456557
210 0.0472885
225 0.0488768
240 0.0503814
255 0.051868
270 0.0533207
285 0.0547436
300 0.0561625
-And centre of mass:
0 0
15 0.916885
30 1.05944
45 1.16649
60 1.25004
75 1.31444
90 1.37307
105 1.43301
120 1.47879
135 1.52776
150 1.57137
165 1.6211
180 1.64439
195 1.68883
210 1.71222
225 1.75035
240 1.77255
255 1.8117
270 1.83702
285 1.87376
300 1.8958
But still there is more thing - do you how the MSD is normalized? Because I
have compared mass weighted MSD calculated using Gromacs tool and nMoldyn and I
get the same difference for all my cases (simulations of 2ns, 15ns and 150ns)-
in the latter diffusion constant is twice the value of the one obtained in
Gromacs. So I expect the difference in normalization.
OK, but we need to see your terminal command lines in order to eliminate
your use of the tool as a source of the problem. They should be at the
top of the .xvg file, if nowhere else.
Mark
Cheers,
Slawomir
On 6/12/2011 3:58 AM, S“awomir Stachura wrote:
Hi,
There is something interesting concerning these MSD calculations. If I treat
Centre of Mass MSD if it'd be expressed not in nm^2/ps , but Angstroms^2/ps, I
get ideally the same results as for mass-weighted ones. And it's true for all
my three cases, in which I performed simulation of different times. Is that
possible there is some bug in MSD? Because as for me it looks so....
I would be amazed if GROMACS did this. Can you copy and paste from your
terminal to show this?
Mark
Hope to have someone join the discussion,
Slawomir
Wiadomo¶æ napisana przez S“awomir Stachura w dniu 2011-12-04, o godz. 22:38:
Hi,
I was just wondering how MSDs in Gromacs are normalized. I am calculatiing MSDs
for my lipid system of different timesteps of simulation and I get much higher
results for centre of mass calculations in comparison to mass-weighted one.
And I thought about normalization issue, but I couldn't find any informations
concerning that topic in manual.
I'd be grateful if someone could explain how mean square displacement is
normalized.
Cheers,
Slawomir
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