[gmx-users] Trajectory has one atom less

Alexander Alexander alexanderwien2k at gmail.com
Fri Aug 5 09:16:06 CEST 2016

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?

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