I am trying to implement fene potential between bonded pairs in a protein structure. I have the distance between the pairs in native state in crystal structure. How can I use this in lamps fene bond calculation. In fene potential my r=(rij-rij_crystal) where rij is distance between I and j and the other one is the distance in native state. In lamps its just rij. Do I implement it on my own in the code or its inbuilt? Plz let me know.
LAMMPS cannot do what is not mentioned in the documentation. Thus if you want a different FENE bond potential function, you need to do your own C++ programming and implement a suitable variant.
You don’t need to implement a new potential style. Your r_\text{ij,crystal} distance is related to the \sigma in the LJ potential via the relation r_\text{min}=2^{1/6}\sigma, as everyone knows. Besides reading the documentation, try plotting the bond_style fene potential with your fav program (mine is gnuplot), and see how the potential parameters interact together.
Thanks for the suggestion. If I am giving zero value to the coefficients corresponding to the lj potential in fene as I wanted to consider purely fene, can it still be done without implementing by myself. I am just thinking that these simulations are very common, so it must be inbuilt in lammps. I am new to lammps, and I may not know.
What do you mean? If you are not able to describe your problem, there is no way you can solve it. Also, do not expect other people to do the work for you.
What is available in LAMMPS is described in the documentation. We take great care that no usable feature is undocumented. Any documented feature that does not work as documented is considered a serious bug and will prompt a correction of the code or the documentation. So if you believe what you want to do is a common occurrence then it has to be possible with what LAMMPS offers already.