[gmx-users] doubt in PCA?

[Seera Suryanarayana]

Dear gromacs users,
I just want calculate the free energy difference between two
successive trajectories. As I know first we have to generate
contrivance matrices by using gmx covar and then have to execute the
gmx anaeig for eigenvector analysis. Here my doubt is how to give my
interest of trajectories? Suppose I want to have the free energy
difference between conformational sub state at 29800ps  and
conformational substate at 29900ps trajectory. How do I select these
two substaes in gmx covar and gmx anaeig? Kindly help me in this
regard.

Thanks in advance
Surya
Graduate student
India.