I am trying to reproduce the Rouse modes free energy curve using ABF. I have already run the standard all-atom simulation and plotted the simple Boltzmann inverted free energy of the first Rouse mode. The plots have been pasted below:
Now, I am trying to run the ABF calculation for the simulation, using the same LAMMPS settings and data file I used for creating the plots I have posted above. I am running four independent simulation for 5e+6 timesteps. My JSON file for ssages is:
I am trying to reproduce the Rouse modes free energy curve using ABF. I have already run the standard all-atom simulation and plotted the simple Boltzmann inverted free energy of the first Rouse mode. The plots have been pasted below:![f_x1](https://github.com/SSAGESproject/SSAGES/assets/68096065/02d8bc46-311e-481c-ae04-3278b24b46bb)
Now, I am trying to run the ABF calculation for the simulation, using the same LAMMPS settings and data file I used for creating the plots I have posted above. I am running four independent simulation for 5e+6 timesteps. My JSON file for ssages is:
The free energy curve i obtained after running the integrator![RouseMode1_integrated](https://github.com/SSAGESproject/SSAGES/assets/68096065/8d63ac0f-37a0-4a10-a9d9-7c0ee4de1fb7)
ABF_integrator.py -i Force_ABF.out -o ABF -p False -n 1000
was:This is entirely off. I don't quite understand what I am doing wrong. What is the method for plotting the ABF curve for the first Rouse Mode?
If it is of any use, my LAMMPS unbiased MD settings and data files (with a .txt extension) have been posted here.
I just wanted so say: I appreciate all the help you have provided here!! sys.gaussianpolymer.data.txt sys.gaussianpolymer.settings.txt