[gmx-users] Re: gmx-users Digest, Vol 92, Issue 49

[Sławomir Stachura]

Ah, OK. The commands I used were:

g_msd -n POPC_index.ndx  -lateral z -o POPC_150ns_CM_MSDlat.xvg -mol diffmol.xvg
g_msd -n POPC_index.ndx  -lateral z -o POPC_150ns_MW_MSDlat.xvg


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> Message: 2
> Date: Fri, 09 Dec 2011 12:36:49 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re:Re:Re: MSD normalization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4EE16631.2030306 at anu.edu.au>
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> 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
>