[gmx-users] Trajectory has one atom less

[Teemu Murtola]

What atoms do you have in your groups A and B? Without the -fgroup option
(new in version 2016), Gromacs tools only support trajectories that contain
the first N atoms from the topology file. The trajectory file does not
contain atom indices.

So if your groups have other atoms than 1-18109, you cannot use a
trajectory that contains only them together with the original topology.
Prior to 2016, you can possibly create a topology for your subset with
convert-tpr, and also update your index file to match the new topology.

Best regards,
Teemu

On Fri, Aug 5, 2016, 10:16 Alexander Alexander <alexanderwien2k at gmail.com>
wrote:

> Dear gromacs user,
>
> From my case.xtc I am just interested in two groups (A and B) of it to have
> in my "case_noPBC.xtc", so, I make a case.ndx file to choose them together
> in "gmx trjconv ... -f case.xtc ... -n case.ndx ...". In all of the above
> steps I see the total atoms number of two groups together is 18109 which is
> expectedly the sum of the two required groups atoms (A 109 + B 18000).
> But when I invoke "gmx pairdist -f case_noPBC.xtc ... -ref B -sel A ...
> -selgrouping ...", an unknown inconsistency happens just because of one
> atom difference as below:
>
> Inconsistency in user input:
> Trajectory has less atoms (18109) than what is required for evaluating the
> provided selections (atoms up to index 18110 are required).
>
> Do you know why, please?
> Thanks
> Alex
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