hi
I am here with a basic question . I have extended and appended a simulation run, but the final trajectory i got is shorter than expected. Do i need to merge all gromac backed up trajectory files to make a complete one?
To append in gromacs, all you need to add -append yes
For example, you run a simulation with KLM.tpr file using
gmx mdrun -deffnm KLM -cpi KLM
If you happened to stop it, you continue using CPI file by changing the bash file to
gmx mdrun -deffnm KLM -cpi KLM -append yes
Yes Dr. Teslim I did that . But somehow I am not getting complete simulation. Seems like extend doesn’t resume the trajectories from the last point. Do I have to catanate it or extend take care of that itself
If you have two different xtc files, you can concatenate. For your situation, you need to check your nsteps. you might have made mistakes. Check it very well
To combine two files, see this explanation. For a 100 ns simulation, you can create two files of 50ns each. The second should have an initial step that corresponds to 50ns and runs for 50 ns to make 100 ns.
1st xtc file - Run-ONE.xtc
nsteps = 500000
dt = 0.002
2nd xtc file - Run-TWO.xtc
nsteps = 500000
dt = 0.002 ; 2 fs
init_step = 500000
gmx trjcat -f Run-ONE.xtc Run-TWO.xtc -o Run-ALL.xtc