[gmx-users] Re: Regarding mean square displacement

[Kavyashree M]

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?

Thank you
Kavya

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
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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