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Bug #161

timestep discrepancy in g_angle and g_covar

Added by Fabio Affinito about 12 years ago. Updated about 12 years ago.

Status:
Closed
Priority:
Normal
Category:
analysis tools
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Hi,
I sent the following email to the gmxusers list. Then David suggested to report this bug. I hope that could be useful.

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?

Thanks!

Fabio

History

#1 Updated by Berk Hess about 12 years ago

You don't say how you generated the two trajactories,
so I can not say if timestep information has been lost.

mdrun writes correct times and so does trjconv.

Berk.

#2 Updated by David van der Spoel about 12 years ago

Fixed minor bug in g_angle (in CVS). Now the time step is correct.

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