Creating lammps data file using topotools

Dear users,
I have a confusion of simulating ZnO monolayer using reaxff. I have made a ZnO monolayer using vesta then converted it to lammps data file using vmd topo tools. But here my doubt is when I am converting it to lammps data file topotools takes one of the default force field (which I dont know) which is not obviously reaxff. So using this default forcefield to preapare the system and again using different force field (reaxff) to simulate the structure is not the wrong way to do? So I think I can not prepare ZnO lammps data file other than defining explicitly inside lammps input script. Please help me to sort this out.
Regards
Sasthi

Dear users,
I have a confusion of simulating ZnO monolayer using reaxff. I have made a ZnO monolayer using vesta then converted it to lammps data file using vmd topo tools. But here my doubt is when I am converting it to lammps data file topotools takes one of the default force field (which I dont know) which is not obviously reaxff.

The VMD TopoTools plugin ignores the force field and only inserts commented out dummy entries.

So using this default forcefield to preapare the system and again using different force field (reaxff) to simulate the structure is not the wrong way to do? So I think I can not prepare ZnO lammps data file other than defining explicitly inside lammps input script. Please help me to sort this out.

you are thinking wrong. preparing a data file for use with ReaxFF using TopoTools is about the easiest conversion, since you don’t need to do any atom typing (just assign elements) and you don’t need any topology information (just write out the data file in atom style charge).

axel.

Thank you axel for the clarification. Now what I think that for the atom style charge no bonds, dihedrals, impropers etc. are there so topotools does not need any force field of conversion from pdb to lammps data file. But I think for atom style full for any other system the force field is required.

I am sorry if my thinking is wrong again.Thank you again.
Regards
Sasthi

Thank you axel for the clarification. Now what I think that for the atom style charge no bonds, dihedrals, impropers etc. are there so topotools does not need any force field of conversion from pdb to lammps data file. But I think for atom style full for any other system the force field is required.

you are thinking wrong again. please see the documentation and tutorial materials about TopoTools, which provide examples to e.g. set up simulations for OPLS/AA.

axel.

please also keep in mind, that TopoTools was not explicitly written for LAMMPS but for use with a variety of MD software packages. It very deliberately (like VMD) is force field agnostic, and it depends on users knowing what they are doing. indeed, one of the main motivations is to be different from other tools that often make certain assumption and make choices for the user. that is ok under many circumstances, but it can become a problem, when trying to do something non-standard.

the fact, that one can write scripts on top of TopoTools to, e.g., read or write LAMMPS data file (but not only those) is an additional feature, but not its main purpose and for certain, it is not meant to be a fully automatic, do-the-right-thing converted from coordinate files to topology files. that cannot be, since most coordinate files (like PDB files, which are a very, very bad choice, BTW) are missing a lot of information, TopoTools (or rather VMD that it relies on) can only use the information available. there are add-on functions to apply certain heuristics to guess missing data, but the correctness of that is depending on the information provided. and sometimes, heuristic topology generation will give wrong results. of course, heuristics are dependent on the choice of force field. for example, the (partial) charge information that is crucial in many molecular force fields is missing in PDB or .xyz files and there is no simple way to recover that information heuristically. OPLS/AA has an “increment system” where those can be computed based on the specifics of the atom type assignment, which must be done by a human (although it can be scripted) for each particular case.

axel.

Thank you axel. I will go through the tutorials.