[gmx-users] Project trajectory without fitting using g_anaeig

[Tsjerk Wassenaar]

Hi Bob,

>From reading the source code gmx_anaeig.c it seems that the fitting is
only performed when a fit-structure is present in the eigenvector
file. That means that -proj should give what you want as it is. The
help seems to incorrectly state that the reference is used for fitting
if a fit-structure is not present in the eigenvector file. Probably
one of the developers should have a look at this.

Best,

Tsjerk

On 9/27/07, Robert Johnson <bobjohnson1981 at gmail.com> wrote:
> 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
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623