Combination rules or tabulated potentials?

User discussions
1

GROMACS version: 2019.6
GROMACS modification: No

Dear all,

As part of my project I am working with hybrid simulations, combining atomistic and CG representations. In my particular case, I work with a system using CHARMM36 and MARTINI. Searching in the literature, finding the optimal coupling scheme between the AA and the CG regions is still an on going area or research. Some authors uses tabulated potentials, other use the standard combination rules, together with virtual sites to bridge the AA/CG interactions.
So my question is, when to use tabulated potentials and when combination rules are sufficient, to account for the non-bonded interactions?

Thanks in advance,
-Yasser

2

Hi,

So my question is, when to use tabulated potentials and when combination rules are sufficient, to account for the non-bonded interactions?

That depends

  • on the functional form that you use to describe your non-bonded interactions. If the functional form is implemented in GROMACS you do not need to generate tabulated potentials, if the functional form is not implemented you need to use tabulated potential
  • on the force field philosophy behind the generation of non-bonded parameters. Are combination rules used to generate parameters between different particle types? Then you can use them, in place to generate all the parameter combinations.

That is a general consideration for any type of non-bonded interaction between particles.

See here more on non-bonded interaction
http://manual.gromacs.org/current/reference-manual/functions.html

and combination rules

http://manual.gromacs.org/current/reference-manual/topologies/parameter-files.html

best regards
Alessandra

3

Thank you very much!

Best,
Yasser