[gmx-users] gmx trjconv trr xtc

Alex alexanderwien2k at gmail.com
Tue Mar 12 00:56:38 CET 2019

Dear groamcs user,
A system of mine contains two molecule type of A and B in water. Using
gmx trjconv -f out.xtc -o out.last.5ns.trr I  first truncated the last 5ns
of the system's XTC file as a TRR file and just selected the non-water
contents so that the TRR file only has A and B. The TRR file is 4.4 GB.
Then I applied again the "gmx trjconv -pbc cluster -center yes -f
out.last.5ns.trr -o out.last.5ns.xtc" and again just non-water was chosen.
I was expecting that the both out.last.5ns.trr and out.last.5ns.xtc would
have the same size 4.4 GB as the material in both of them are just A and B,
however, the out.last.5ns.xtc is just 1.4 GB!
I wonder if that is normal? here I just care about the coordinates
dynamically and not velocity, do you think I am loosing any coordinate in
by the second command from out.last.5ns.trr to out.last.5ns.xtc?


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