[gmx-users] fitting of the RMSD matrix
mike.nemec at uni-due.de
Thu Jan 19 13:48:08 CET 2017
Dear GROMACS mailing list,
I want to calculate a 2D RMSD matrix using g_rms of gromacs v4.6.7
(1) between all frames of one trajectory and
(2) between all frames of two different trajectories.
I figured out, that this is possible by
g_rms -f traj.xtc -s traj.tpr -m RMSD_matrix.xpm -bin RMSD_matrix.dat
either specifying a second trajectory by -f2 or not, where the RMSD
matrix is obtained in binary format in the installed precision
(RMSD_matrix.dat). Unfortunately, the manual gives only the information
about the RMSD traces, that they are fitted to the reference, but I did
not found any information about the RMSD matrix generation.
My question concerns the fitting/superimposing:
Is the RMSD matrix calculated by
(1) fitting all structures to the reference submitted by -s
(2) or by a pair-wise fit between all structures for which then the RMSD
values are calculated?
If it is not done by a pair-wise fit, is there an option to achieve a
pair-wise fitted RMSD matrix?
Thank you in advance,
More information about the gromacs.org_gmx-users