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 <jalem...@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 <hmkv...@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
--
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Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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