lammps data file - vmd- file converting

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1

Dear Lammps users,

I am going to import information of an epoxy molecule to lammps. this molecule has been designed with Avgadro. This epoxy molecule has 46 atoms, 47 bonds, 81 angles and unfortunately 110 atomic torsions which means 110 Impropers and dihedrals(totally). So, calculating Impropers and Dihedrals could be very time consuming.

So, I was thinking to find a faster method. Then I noticed that VMD can prepare Lammps file format from PDB file prepared by Avgadro.

However, when I take Lammps file format from VMD, dihedrals and Impropers report as ZERO which are not correct.

So, my question is which systematic method I should follow to import this molecule information data to Lammps.

Yours Sincerely,

Bahman

Material Design group, Helmut Schmidt University, Hamburg

Bahman Daneshian

2

You can use topotools plugin in VMD to generate lammps data file. There are options to guess dihedrals and impropers present in the molecule.

Santhosh…

3

the primary issue is to use a PDB intermediate file format. that file format does not store any topology information. and it is generally one of the worst file formats to exchange data with (it has size limitations, stores coordinate in very low precision and is lacking a lot of important information). after discarding this information, it is impossible for VMD to know it and hence TopoTools cannot know it either. it will try to reconstruct the bond information based on some heuristic that is not always 100% accurate, but most of the time sufficient for visulization purposes.

it is often possible to reconstruct the remaining topology data based on the bonding patterns, but this is only as good as the (guessed) bond information in the first place. thus using a file format that maintains all this information that you entered is the best solution.

axel.

4

Thank you for the information.

5

This use-case is also one of the main features of vipster
(https://github.com/sgsaenger/vipster).
By default, it generates bonds automatically, which you can control
with the bond cutoff factor in the Settings tab and the bond cutoff
radius for your (file-specific) atom types in PSE tab.
When you export a lammps data file, you can request angles, dihedrals
and impropers to be generated according to the generated bond
topology.

Regards,
Sebastian