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