[gmx-users] Estimation of the trajectory sampling from Covariance analysis

[James Starlight]

Dear Gromacs users!


In the gromacs manual I found that "A good way to check the relevance
of the first few principal modes is to calculate the overlap of the
sampling between the first and second half of the simulation."
Below you can see results of such overlap (inner product) between 2
sub-spaces calculated from first and second part of my trajectory ( in
the lowest frequency regime- only first 5 principal modes from both
trajectories)


                                                    MD Second Half of simulation
                                                      #1     #2     #3
    #4     #5
MD first Half of simulation #1   +0.21  +0.68  +0.36  -0.33  -0.37
MD first Half of simulation #2   -0.07  +0.13  +0.57  +0.30  +0.02
MD first Half of simulation #3   +0.16  -0.22  +0.31  +0.20  -0.28
MD first Half of simulation #4   +0.85  +0.22  -0.07  +0.02  -0.14
MD first Half of simulation #5   +0.14  +0.40  -0.37  +0.49  -0.13


Here you can see that 4rd PC from the first half of simulation
correspond to the 1st PC from second half of simulation (+0.85). On
the contrary 2nd mode from second half of simulation correspond to the
1st mode of first part of simulation (+0.68 ). Finally 3rd mode from
second half of simulation corresponds to the second mode of the first
mode. So it seems that during simulation there is some 'dynamics' in
the lowest frequency regime (e.g I noticed that SEVERAL high frequency
modes in the shorter trajectory during evolution of the system  join
together forming ONE more slower mode in the longest trajectory). How
this can be described from the physic points of view? And how exactly
I can estimate the sampling quality of my complete trajectory ?

Thanks for help,
James