[gmx-users] Re: Regarding mean square displacement

Kavyashree M hmkvsri at gmail.com
Thu Feb 7 05:49:13 CET 2013

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.

Kindly reply

Thank you

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

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