![]() ![]() TopoTools (same as VMD) knows nothing about specific force fields or atom types or types of bonded interactions and how to assign them. To produce suitable output files, it has to assume that you have done and correctly entered the forcefield atom typing and bond topology information beforehand. It just offers tools to conveniently enter and modify topology related data, plus commands to write out topology files in multiple formats. Like VMD, TopoTools is for the most part completely agnostic of the force field. the partial charges need to be determined in accordance with the force field you are using. but then again, the major issue at hand is a matter of understanding force fields and how to use them correctly and less so how things need to be done with TopoTools or LAMMPS.the the vmd mailing list would be more suited. ![]() Please note that this is mostly the wrong forum. However, the number of dihedral types and improper types are different from those generated by TopoTools. Subsequently, I try to find out the force field parameter, such as pair_coeff, bond_coeff, angle_coeff, dihedral_coeff, improper_coeff from. I am wondering if that is the way to calculate the charge as in TopoTools. Each partial charge is calculated by involving the electrovalency, electronegativity, both number of bonding and non-bonding electron. ![]() I just developed the LAMMPS data file for benzaldehyde phenylhydrazone using TopoTools, as shown below. Sorry if I ask the following questions in this forum. ![]()
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