Topology file for all atoms in unbound state

User discussions
1

GROMACS version: 2024
GROMACS modification: No

Similar to this one, but just atoms: Topology file for metal ion - #6 by milosz.wieczor

I can implement these manually:

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon ; sigma_14 epsilon_14

however, I am lost where do we get the values for: sigma epsilon ; sigma_14 epsilon_14

2

following up, tnx

3

In GROMACS, the parameters sigma and epsilon are related to the Lennard-Jones potential, which describes the non-bonded interactions between atoms. These parameters determine the van der Waals interaction between atoms. The sigma parameter represents the finite distance at which the inter-particle potential is zero, and epsilon represents the depth of the potential energy well.

The sigma_14 and epsilon_14 parameters are used for 1-4 interactions, which are the interactions between atoms separated by three consecutive bonds. The 1-4 interactions are typically scaled compared to the regular non-bonded interactions to account for the fact that they are part of a closer chemical environment.

To obtain these parameters for a specific molecule, you would typically refer to force field parameters. Force fields like AMBER, CHARMM, and OPLS, for example, provide parameter sets for various atoms and molecules. The parameters are often derived from experimental data and quantum mechanical calculations.