[gmx-users] content of trr / xtc files + -b/-e flag question + tpr question

[Eric Smoll]

Hello Gromacs users.

I have a few questions.

I ran two small trajectories:

trajectory 1:
dt = 0.0008
nsteps=10
nstxout=2
nstxtcout=3

trajectory 2:
dt = 0.0008
nsteps=10
nstxout=3
nstxtcout=2

We can examine the content of each trajectory using "trajconv -sep -nzeros
1". The initial frame is always the initial coordinates.

In trajectory 1, the trr file contains frames at times
0.    ,  0.0016,  0.0032,  0.0048,  0.0064,  0.008
and the xtc file contains frames at times
0.    ,  0.0024,  0.0048,  0.0072

In trajectory 2, the trr file contains frames at times
0.    ,  0.0024,  0.0048,  0.0072
and the xtc file contains frames at times
0.    ,  0.0016,  0.0032,  0.0048,  0.0064,  0.008

In section 7.3.8 of the manual, under "nstxout" it reads: "*frequency to
write coordinates to output trajectory file, the last coordinates are
always written." **My tests seem to suggest that the last frame of the
simulation is not always written. Am I reading this incorrectly? Is the
final frame always written to the mdrun -c flag as a .gro file? If this was
the intended meaning it is a bit misleading.*

*Many GROMACS tools make use of -b/-e flags. What is the precise rule these
flags apply?* For instance, how would -b  0.0020 -e 0.0068 filter the
results above? What about -b  0.0021 -e 0.0067?

Many GROMACS tools make use of a run input file when processing coordinate
or trajectory files. The run input file contains an initial coordinate set
and mdrun uses the initial coordinates to start a simulation. However, *it
is not clear to me what other tools make use of these "tpr" initial
coordinates. If I am manipulating coordinate and trajectory files, when is
it necessary to update the initial coordinates in a "tpr" file?*

Best,
Eric