i am trying to simulate the solvation of small molecule of 4 monomer alginate polymer.But i can’t hget the dihedral coefficients for the LAMMPS input files.I am new to LAMMPS and am learning it.
The LAMMPS documnetation only exlanis the requied coeffiecnts but doesn’t provide any way or values for the potetntials and coefficients needed in the input file.
That is (mostly) correct and deliberately so. Unlike some other software (e.g. the CHARMM software), LAMMPS is not written for use with a specific force field and a specific class of compounds (like the CHARMM force field). It is simply not possible to provide explanations and parameters for all the many possible uses of the potential functions that are implemented in LAMMPS.
Besides, those are two different steps. The information for specific force fields and how to apply them correctly is described in their corresponding publication(s), so those papers are the primary source for the information you are looking for. They explain what the parameters are, how you need to select and apply them to your specific compounds. In some cases, this step can be automated, for example with proteins. Then a specific software is required that uses heuristics (e.g. naming conventions established by entities like the protein data base PDB) and a database with pre-assigned molecule fragments and then uses this information to build a topology and assign force field parameters. LAMMPS does not include such tools, and - as mentioned above - that is a deliberate choice. For some cases, there are converters that can be used to convert the output for a force field specific topology builder tool into a format that LAMMPS uses. But those are very application specific and may or may not work correctly for your case. There is some additional information along those lines here: 8. Howto discussions — LAMMPS documentation
Bottom line, what you are asking about is something that is not part of LAMMPS, but part of learning MD and MD with force fields. Please discuss with your adviser/supervisor/tutor to be properly trained in how to apply the force fields in simulations. It is not even LAMMPS specific, since you could do the same simulation with other MD programs that have the same potential functions available (e.g. Gromacs, NAMD, OpenMM) and there you would have the same problem.