Accessing 1-4 interactions

LAMMPS LAMMPS General Discussion
1

Is there any way to access the 1-4 pairs which lammps calculates internally via the special bonds command ?

Thanks
Arun

2

Can you be more specific about how you want to access this information and for what purpose?

3

Hello Axel
Thank you for your reply. I am trying to convert a LAMMPS data file to a GROMACS topology file. The size of the system is about 60000 atoms. The GROMACS topology file contains a section exclusively for 1-4 interactions called the [pairs]l section while LAMMPS calculates this internally. If I can access the 1-4 list of each atom from LAMMPS I should be able to fill in this section of GROMACS.

4

LAMMPS determines the 1-4 (and 1-2 plus 1-3 neighbors) internally at runtime and distributed across MPI processes. They can currently only be accessed directly from C++ as Atom::special. Special neighbors are also encoded into the neighbor list in the top two bits (also at runtime) and can be accessed through post-processing the neighbor list information (which is also per MPI process data).

This information is not too complex to be generated directly from a script when you have the bond topology information. We have done that for converting CHARMM inputs from NAMD to Gromacs with the VMD TopoTools plugin: http://dx.doi.org/10.1021/acs.jcim.6b00103
topotools/topogromacs.tcl at f33e3756ad7946f76452d95e586124eb9dc2e88f · akohlmey/topotools · GitHub

5

Yes I was trying to bypass writing a script. But I will look into what you sent

Thanks Axel