[gmx-users] How to use different reference structures for g_covar and g_anaeig

sridhar at cdfd.org.in sridhar at cdfd.org.in
Wed May 16 18:34:26 CEST 2007

Dear All,
I have two specific questions:

1.I have been to do COMBINED ESSENTIAL dynamics by concatenating two
trajectories. I calcualted the covariance matrix using the default options
of g_covar. This should presumably use the average structure for fitting.
Now I want to use one of a different structure other than the average
structure of the two trajectories in g_anaeig. It was said in the
gmx-mailing lists that g_anaeig uses the structure in the eigenvec.trr
file if present, otherwise it takes the structure given in the -s option.
But I suppose the structure file is always present in the eigenvec.trr
file. Is there any way that we can ignore the structure file in
eigenvec.trr file and use the file supplied in -s option of g_anaeig?

2. Further, in the case of COMBINED ESSENTIAL DYNAMICS, many researchers
could compute the Mean square fluctuation by individual trajectories
projected on to the combined eigenvectors using the covariance matrix. Can
any one explain how to calculate this?
g_anaeig of COMBINED ESSENTIAL DYNAMICS can give eigenrmsf of only the
combined trajectory!


More information about the gromacs.org_gmx-users mailing list