[gmx-users] extracting a list of frames from a trajectory

[Mark Abraham]

Hi,

Sadly there's nothing to be done except ignore the field or do multiple
passes. The history of trjconv is a large number of people adding features
convenient for their use case, and not knowing how it interacts with the
huge surface area of the set of all other features. So the person who
wanted such automatic regularisation trips the implementation of -fr, etc.

Mark

On Fri, 13 Jan 2017 14:22 Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> I’m trying to extract a list of frames from a long trajectory:
>
> gmx trjconv -f complete.trr -s nvt.tpr -novel -ndec 14 -fr frames.ndx -pbc
> atom -o conf_test.gro -sep
>
> where frames.ndx contains the following:
>
> [ frames ]
> 2 3 4 5 6 8 ...
>
> Each frame is supposed to be separated by 10 ps, so that for frame 2, t=
> 20.0000. Hence, conf_test1.gro starts with "Generated by trjconv : Protein
> in water t=  20.00000”, which is what we expect. However, the timestamps in
> the subsequent files are:
>
> Generated by trjconv : Protein in water t=  30.00000
> Generated by trjconv : Protein in water t=  40.00000
> Generated by trjconv : Protein in water t=  50.00000
> Generated by trjconv : Protein in water t=  70.00000
> Generated by trjconv : Protein in water t=  80.00000
> …
>
> while it should have been 30, 40, 50, 60, 80, .... This happens a lot of
> times throughout the whole list of frames. Why does it happen? How can I
> fix it?
>
> Best,
> Irem
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