[gmx-users] dPCA - trajectories

[Fabio Affinito]

Dear all,

Using

g_angle -f ../trj1_0_100.xtc -s ../g_prot.tpr -n test.ndx -or -type 
dihedral -e 10000

As expected, I obtained the following statement

[cut]
Group     0 (    Backbone) has   664 elements
There is one group in the index
Reading file ../g_prot.tpr, VERSION 3.2.1 (single precision)
Last frame      25000 time 10000.000
There are 166 dihedrals. Will fill 111 atom positions with cos/sin
[cut]

Then, when using the covariance analysis

g_covar -f traj.trr -s dummy.gro -nofit

It seems like the trajectory is of a different length, because a 
different timestep seems to be used:

[cut]
Calculating the average structure ...
trn version: GMX_trn_file (double precision)
Last frame      25000 time 25000.000

Constructing covariance matrix (333x333) ...
Last frame      25000 time 25000.000
Read 25001 frames
[cut]

I suppose it's just because in the new trajectory the information of the 
timestep length is lost. Am I right?

Thank you,

Fabio