[gmx-users] dPCA - trajectories

[David van der Spoel]

Fabio Affinito wrote:
> 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?
I think so. Could you please submit a bugzilla? Otherwise this will most 
likely not be fixed.

> 
> Thank you,
> 
> Fabio
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se