Hi,
I have a trajectory file which is 100 GB. I have run simulation for 25ns. Now I want to analyse the structure with the app which I have build. I want to split this file in 25 pieces(for each 1ns). I used command "gmx trjconv -f traj.trr -s next25.tpr -o protein.pdb -split 500" but it gives error "segmentation fault,core dumped. I think this is due to memory limit,is it right?
Is there any other way to split this file?
When I try to convert it to pdb everything works fine and it creates 200 GB pdb file. I think, this is because my velocity coordinates also present in trajectory, is there a way to get rid of them during convertation to pdb file?
Thanks in advance.
It's memory. You can take .xtc file for analysis. or you can do it simply by below command.
gmx trjconv -s file.tpr -f file.trr -o file_t1.trr -b t1 -e t2
t1= start time
t2= end time
In this way, you'll get the trajectory between t1 and t2 timescale and split into short trajectories.
It is a common practice to split an MD trajectory into short "windows" on the fly.
Other option is to use gmx trjcat.
gmx trjcat -f file.trr -b start time(ps) -e end time(ps) -o output.xtc
Understood,
I was using the same command
gmx trjcat -f file.trr -b start time(ps) -e end time(ps) -o output.xtc
but saved -o as pdb, so it was generating empty file
Thanks
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