[gmx-users] Re:Re:Re: MSD normalization

[Sławomir Stachura]

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.

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
>