[gmx-users] Re: Regarding mean square displacement

[Justin Lemkul]

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
>>>> 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>
>>

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

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

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