[gmx-users] dPCA - trajectories

Fabio Affinito affinito at sissa.it
Tue Aug 28 11:13:44 CEST 2007

Dear all,


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

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

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:

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

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

Thank you,


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