[gmx-users] Re: Re: msd of com of bilayer

[Patel Ronak Y]

Dear Dr Spoel,

I used g_traj for calculation of com of bilayer.

For calculation of msd I used

    |r(t)-r(o)|^2
msd=------------
         4
                      r(t)=coordinate at time t
                      r(0)=coordinate at time 0

to calculate msd along x and y direction independently. The graph shows
increasing and decreasing patterns instead of just increase that is
expected.

Is there anything wrong in my calculation? or is it due to the saving time
for trajectories is 4ps that I used?

> Dear all,
>
> How can I calculate Mean squared deviation of center of mass of system
> (lipid bilayer).

check g_traj

>
>