Tools like towhee, moltemplate, emc, AmberTools, (msi2lmp) use the atom type names of the participants atoms to generate angles, dihedrals, and impropers, as well as look up their force field parameters.
If some of of the dihedral parameters seems wrong to you, then it might mean that you have assigned the wrong atom type (type-name or type-integer) to some of your atoms. Unfortunately, depending on which tool you used to build your system, this can be easy to do.
In a force field like OPLSAA, there are dozens of different types of carbon, oxygen, and hydrogen atoms, for example. You must chose carefully.
If you are willing to try using other molecule builders, both "moltemplate" and "emc" support the OPLSAA force field. (Disclaimer: I wrote "moltemplate")
If you know of a general tool that can read PDB files and automatically decide which type of carbon, hydrogen, oxygen... atoms should be used (from only the information in the PDB file), then please post a reply here.
P.S. It is possible to have OPLS dihedrals with ALL 4 of the parameters (K1, K2, K3, K4) set to zero. These dihedrals have no effect, but some force-fields insist on defining dihedrals every time 4 atoms are bonded together. These unnecessary dihedrals slow down the calculation slightly, but they are relatively rare. (They appear in less than 30% of the dihedrals in the OPLSAA force field parameter file. Eliminating them from the moltemplate force field file," oplsaa.lt
", would solve this small problem, but it hasn't been a priority for me to do that so far.)
Dear lammps User,
I used MCCCS towhee to set up the system, and continue to equilibrate in LAMMPS. There are some problems in the data file form Towhee, the first parameter of dihedral is 0. I looked through all the dihedral style in lammps and the first parameter in dihedral style always represent energy, is there any possible the first parameter of dihedral is 0? What dihedral style that I can find for these parameters is OPLS.
The parameter of dihedral is pasted:
1 0.0 1 0 0.25000000000000000
2 0.0 1 0 0.0000000000000000
Is there any one can give me some advice? Any help would be appreciated.
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