[gmx-users] Project trajectory without fitting using g_anaeig

[Robert Johnson]

Hello everyone,
I'm performing PCA on single stranded DNA adsorbed to a carbon
nanotube which is aligned along the z-axis. Because the DNA is
adsorbed, fitting each frame to the average structure via a 3D
translation and rotation doesn't make sense. In my analysis, I
minimize the RMSD between each frame and the average DNA structure by
the following algorithm:

1. Translate instantaneous DNA structure along the z-axis such that it
has the same center of mass z-component as the average structure (i.e.
z_com = z_com_avg)

2. Apply a rotation about the nanotube axis to minimize the RMSD
between the instantaneous and average structures.

I perform this fitting on each frame of my trajectory using scripts
that I wrote for VMD and save the resulting RMSD-minimized trajectory.
I then construct and diagonalize the covariance matrix using the
following command:

g_covar -s average.pdb -f fit-trajectory.xtc -nofit -noref

Here, average.pdb is the average DNA coordinates. Since I have already
manually fitted my trajectory, I use the -nofit and -noref flags.

Now, I would like to project my fitted trajectory along the
eigenvectors obtained from g_covar. However, it seems that g_anaeig
will automatically fit your trajectory to the first frame in
eigenvec.trr. Since I have already manually fitted my trajectory, I
want to skip this additional fitting step. However, it doesn't seem
like there is a way to do this. Does anyone have any suggestions about
how I could proceed?
Thanks,
Bob