[gmx-users] Re: Regarding mean square displacement
hmkvsri at gmail.com
Thu Feb 7 12:49:40 CET 2013
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?
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.
> 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
> 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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