Hello,
I am simulating a coarse grained polymer chain using LAMMPS. now i am stuck because of one potential that is purely repulsive pair potential between two beads.
potential is like this
E = sum over all beads [ epsilon.{ ( sigma / r)**6} ]
value of epsilon and sigma are known for me.
I dont’t know what LAMMPS cammand i should use for this potential.
please help me.
How about this one: pair_style buck command — LAMMPS documentation ?
I also thought about Buckingham potential and set A and rho coefficient zero but i have one doubt that can i put negative value for coefficient C ?? usually everywhere coefficient or values in pair_coeff we put positive value in the Lammps.
Setting rho to zero would be a bad idea. You don’t want to divide by zero. It would be irrelevant otherwise since multiplying by zero would turn off that term anyway.
In typical Buckingham settings the r**6 term is attractive not repulsive.
Thankyou for your quick response.
can you tell me some other alternative or settings during installation of Lammps ?
Why?
actually i am working on a polymer CG model which have this interaction and i am calculating radius of gyration of the polymer but it is not give the correct value even same polymer when i use in different coarse grained model it give right Rg value so i am not understanding why Rg is not currently from privious CG model. I am working from a month on this model everything i checking all parameters are right but when i am calculating Rg that give we wrong value …that why i am little bit disappointed.
You are not making much sense here. If you are using the Buckingham pair style with A=0.0, rho=1.0, and C = - \epsilon \sigma^6, you will get a repulsive LJ r**6 term.
The fact that you are not getting the expected results is a completely different issue and can have many reasons. How much time you spend on this problem is an indication that you have not yet understood it. Obviously you are overlooking something, but from remote it is impossible to tell you what.
The most common situation, that I have seen with people like you that do not get expected results, is that they are overly confident having done everything correctly. There rarely is a “magic” command in LAMMPS that can “fix” such a situation. You have to go about this the old fashioned way and verify and test every detail of your simulation independently. If you are inexperienced in performing simulations, you need to get tutoring and advising from somebody with more experience. Asking in a forum like this is not going to be very helpful in that kind of situation since this is not a problem of the software itself but about the research itself.
Yes … you are right I am definitely doing something wrong at the understanding level. LAMMPS is software that give results according to my inputs. I will improve my knowledge. Thankyou for your feedback and suggestions.