1-4 pairs and non bonded list

User discussions
1

GROMACS version: 2019.6
GROMACS modification: No

Hi all,

I am currently running tests on reproducing the calculation of a protein in vacuum that was run using the amber14sb forcefield. I am writing the topology manually and comparing to the one where I run calling the forcefield itself. I know this seems redundant, but it will be important for my future work. I have a pair list defined with parameters and a non bonded section (nexc=3). Question is, are the 1-4 interactions counted twice with this set up? Or is it only taken from the [ pairs ] section since I have nexc=3? If the 1-4 is counted twice, then how do I make sure it is only taken into consideration once?

This is the topology file:
processedNa_f2sig05eps_explnb.top (145.9 KB)

2

Typically, force fields scale 1-4 interactions by some factor, so they have to be included, but not by conventional nonbonded interaction forms. So by setting nrexcl = 3, 1-4 interactions are removed (excluded). A [pairs] directive adds them back, but tells grompp to incorporate the scaling factors into the actual nonbonded form that mdrun subsequently uses. In this regard, a pair interaction is actually treated more like a bonded interaction than a nonbonded one.

3

Hi Justin,

thanks for the speedy reply. I think I am on the right track then. I have specified the non bonded interactions in [ nonbond_params] and all the 1-4 interactions separately in the [ pairs ] directive of my molecule, which I suppose will then add them back in, like you mentioned. So now the question is, because I need to have different fudge parameters, I have gen-pairs=no and I’m using this format in the pairs section, with V and W in sigma and epsilon form since func=2, right?

extra LJ or Coulomb [pairs] 2 2 fudge QQ (); qi; qj (e), V[7]; W[7]

I can see where to specify the different fudge QQ value, but how do I specify the different fudge LJ value? I’ve combed through the manual, but couldn’t find the answer to that one.

Thanks!

4

You don’t. That’s what [pairtypes] is for. Values there override those generated by the combination rule and default fudgeLJ (I think, please do a single-point energy calculation to confirm, I am not 100% sure if the default fudgeLJ gets applied or not).

5

Then wouldn’t that be the same as having everything explicitly in the [ pairs ] directive of the molecule as above but then giving epsilon values divided by two for fudge LJ=0.5? Given that V (r) = 4eps [(sig/r)^12-(sig/r)^6].

6

“The normal pair interactions, intended for 1-4 interactions, have function type 1. Function type 2 and the [ pairs_nb ] are intended for free-energy simulations” This is also written in the manual but in File formats — GROMACS 2021.4 documentation [ pairs ] have the possibility of having function type 1 or 2, whereas [ pairs_nb ] have function type 1. Is this correct?

7

Having never used those features, I can’t comment specifically, but type 2 and [pairs_nb] have specific use cases intended for applications related to free energy and corresponding topology transformations. I don’t know how they are interpreted in the context of standard MD simulations.

8

I think I have figured it out. Thank you for your replies, Justin. It’s been helpful to know what the program ignores and overrides when figuring out how to set up my topology.

Thanks!

9

Hi BiaFonseca,

I am facing a similar problem. I understand that including fudgeQQ in [ pairs ] helps consider the scaled-charged interaction. But, how to include the fudgeLJ value in the top file?
Please share your thoughts if you have a working solution.

Thanks,
Pallab