[gmx-users] Concatenating two trajectories

[Monoj Mon Kalita]

Dear Sunita

Are you sure you have added two trajectory files, one from 0 to 40 and the
other from 40 onward ! Because

Here







*Summary of files and start times used:          File                Start
time       Time
step---------------------------------------------------------
complex_prod1_old.xtc        0.000 ps       50.000 ps
complex_prod1.xtc        0.000 ps       50.000 ps WARNING: sameStart time
as previous*


it is saying that you are joining the same two files with same starting
time. However, do you have .trr files, GROMACS generally creates .trr files
for every successful run. You can try to add those .trr files and later
convert them into .xtc files. And you just need to follow like this

trjcat -f 1.trr 2.trr -o all.trr

That is it.

In another case, you said that you are getting strange output in RMSD. Did
you check, is there any broken molecule or not ! sometime the broken
molecule, due to periodicity, leads to strange RMSD outputs.

Thanks

Monoj