[gmx-users] Re: Regarding mean square displacement

[Justin Lemkul]

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
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>

-- 
========================================

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

========================================