[gmx-users] Re: Regarding mean square displacement

Kavyashree M hmkvsri at gmail.com
Thu Feb 7 15:23:14 CET 2013 

Thank you,

My intention is mainly to compare the MSDs of the
trajectory and not the diffusion as such. The paper I
mentioned have used a tetramer for the similar analysis.
Hence I wanted to know whether the values I obtained
is sensible.

Thank you
Kavya

On Thu, Feb 7, 2013 at 7:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/7/13 7:08 AM, Kavyashree M wrote:
>
>> Dear Sir,
>>
>> Yes it is the same protein. Initially I had not superposed the
>> structures in the trajectory. But this time I calculated the msd
>> on a superposed trajectory (of the same simulation). the simulation
>> is carried out on a dimer for 50ns using OPLS-AA and TIP4P water
>> model. Using Gromacs4.5.3.
>> If any other information is required Please let me know.
>>
>>
> The specific suitability of a protocol is dependent upon what you believe
> to be correct for your system based on precedent and chemical knowledge.
>  Also be aware that post-processing of the trajectory to superimpose frames
> defeats the purpose of measuring diffusion - if you re-center or
> superimpose your structures, it's not diffusing!  Dealing with a dimeric
> protein may be a challenge for which g_msd wasn't designed, so I don't know
> if there's an easy solution here.  Perhaps someone else can suggest
> something.
>
> -Justin
>
>  Thank you
>> Kavya
>>
>> On Thu, Feb 7, 2013 at 5:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 2/7/13 6:49 AM, Kavyashree M wrote:
>>>
>>>  Dear Sir,
>>>>
>>>> Thank you for the reply,
>>>>
>>>> It does not cross the boundary. I made the trajectory
>>>> so that the dimers are together.
>>>>
>>>> I again calculated on a superposed trajectory, Then I
>>>> got MSDs in the range of 0.01 to 0.15nm^2. But this
>>>> is still higher than the value mentioned in the paper or
>>>> is this acceptable?
>>>>
>>>>
>>>>  Are you studying the same protein?  Given sparse detail in an email
>>> thread, not knowing whether the simulations were done correctly or for
>>> sufficient time, no one can assess correctness here.
>>>
>>> -Justin
>>>
>>>   On Thu, Feb 7, 2013 at 4:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 2/6/13 11:49 PM, Kavyashree M wrote:
>>>>>
>>>>>   Dear users,
>>>>>
>>>>>>
>>>>>> Since I am getting the mean square displacements in terms of
>>>>>> several nm^2. I doubt it is wrong. Could anyone please explain
>>>>>> me the solution for this. I checked the structure it is not denatured,
>>>>>> In addition I used -rmcomm in order to remove the COM movements.
>>>>>>
>>>>>>
>>>>>>   Sounds like a PBC issue.  Does your dimer split across periodic
>>>>>>
>>>>> boundaries?  If it does, then your MSD is going to go through the roof
>>>>> because it's measuring the MSD of the whole protein.
>>>>>
>>>>> -Justin
>>>>>
>>>>>    On Wed, Feb 6, 2013 at 3:35 PM, Kavyashree M <hmkvsri at gmail.com>
>>>>> wrote:
>>>>>
>>>>>
>>>>>>    Dear users,
>>>>>>
>>>>>>
>>>>>>>     I have a very basic question in MSD calculation.
>>>>>>> g_msd calculation on a protein dimer (~237 aa each)
>>>>>>> trajectory gave a plot of msd, with the values ranging
>>>>>>> between 1 to 14nm^2.
>>>>>>> But is this a sensible MSD? As the values given in a
>>>>>>> paper i was referring was in Ang^2
>>>>>>> J. Chem. Theory Comput. 2012, 8, 1129-1142
>>>>>>>
>>>>>>>
>>>>>>> Command that i used -
>>>>>>>
>>>>>>> echo 3 3 |g_msd -f a.xtc -s a.tpr -o a.xvg -n a.ndx -trestart 10 -b
>>>>>>> 4000
>>>>>>> -e 50000 -rmcomm
>>>>>>>
>>>>>>> Is the range of diffusion coefficient of proteins of in water l
>>>>>>> in the range of x e-5 cm^2/s? (hemoglobin is 0.1 e-5 cm^2/s)
>>>>>>>
>>>>>>> Thank you
>>>>>>> kavya
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>   --
>>>>>>>
>>>>>> ==============================******==========
>>>>>
>>>>>
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Research Scientist
>>>>> Department of Biochemistry
>>>>> Virginia Tech
>>>>> Blacksburg, VA
>>>>> jalemkul[at]vt.edu | (540) 231-9080
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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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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