[gmx-users] Re: Regarding mean square displacement

[Kavyashree M]

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.

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
>>> http://www.bevanlab.biochem.****vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>> <h**ttp://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>
>>> <htt**p://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<h**ttp://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>
>>> <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<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>
>