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lammps full type data file creation

Hi

How can I create lammps data file (full type include bonds , angles dihedrals ...) from pdb file (like topo tools in vmd can do).

for that first an algorithm should guess bonds then angles and impropers and dihedrals. then with the export in type lammps data file in full mod.

problem is that can ovito guess the bonds angles and etc??

If answer is yes ,how?

thanks,

Hi,

That's currently not possible. OVITO can only help you with importing a pdb file, creating bonds and then exporting the atoms and bonds as a lammps-data file with "atom-style full".

 

how can I create bonds?

is it possible I create them manually ?

for example a box of methane , I define bonds for a one molecule and software generalize it to other moleculs?

or define angles dihedrals and etc, manually?

Quote from Constanze Kalcher on September 16, 2020, 10:58 am

Hi,

That's currently not possible. OVITO can only help you with importing a pdb file, creating bonds and then exporting the atoms and bonds as a lammps-data file with "atom-style full".

 

Will there be such a feature in the future ? For any force field

Betim,

As Constanze already mentioned above, OVITO does not have the capability to assign a force field to molecular structures or -more general- to build/construct models and set up simulations. Its current focus is on visualizing outputs from simulations and providing the tools to analyze them.

Our short- and mid-term roadmaps (<=1 year) for developing OVITO are focused on further strengthening and extending the viz and analysis capabilities of OVITO. In the long run, however, we may also consider working on new program features that help building models and setting up simulations. Force field assignment could be one of them. The decision will depend on user demand, the availability of existing solutions (we don't want to reinvent the wheel), and the resources we have available as a business.

Force field assignment is a complex task (as far as I can tell as a non-expert), which is also the reason why users wish to have a highly automatized solution. At the moment, developing such a solution is out of reach for us, because our team does not have the required expertise in that area. However, I hope we can use the next year to acquire the necessary knowledge and build a team that is able to expand OVITO further in this direction.

In the meantime, I can only invite you to express your needs and requirements and let us know what kind of features you wish OVITO to provide in the future. For us it is always helpful to hear how your existing workflows look like and how you would imagine them to be with the help of OVITO.

-Alex