Calculating 1-4 Lennard Jones interactions

User discussions
1

GROMACS version: 5.0.7
GROMACS modification: Yes/No
Hello. I am simulating a united atom model of Polypropylene with TRaPPE UA.
Here are some parts of my topology file:

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 1.00000 1.00000
[ atomtypes ]
;name mass charge ptype V(nm) W(kJ/mol)
CH3 15.0345 0.000 A 0.37500 0.8139
CH2 14.0266 0.000 A 0.39500 0.3818
CH 13.0186 0.000 A 0.46800 0.0828
.
.
.

In the topology file, I haven’t included [pairs]. Only [atoms], [bonds], [angles] and [dihedrals].
Is that enough for calculating the 1-4 Lennard Jones interactions?
Thank you in advance.

2

Hi,
You do not need the directive [pairtypes].
You can look here for more details at File formats — GROMACS 2021.1 documentation
Best regads
Alessandra
PS edited

3

Hello Dr. Alessandra,

I am not sure if the rule is changed for gmx-2021, As per my understanding we need to have an explicit [pairs] section for 1-4 interactions, while yes option in [defaults] simple creates parameters for pairs with defined combination rule. Please correct me, so that I use the correct settings while using gmx-2021.

Regards,
Masrul

4

Thank you, Masrul! @Masrul. You are right. My answer was wrongly formulated. Sorry for the confusion. I will re-edit my post.

The correct formulation is:
the directive [ pairtypes ] is not required (if all 1-4 parameters are generated using the combination rules), but the [moleculetype] directive should be followed by the directive [bonds], [pairs] ect.

Best regards
Alessandra

5

Thank you both for the answers. I tried to do some experiments with a single molecule and up to now I have conclude that:

  • [ pairs ] are useful if you want to use different scaling for 1-4 interactions (e.g. fudjeLJ=0.5). Otherwise there is no need of using [ pairs ]
  • Setting nrexcl=2 will calculate all the non-bonded interactions that are 2 bonds far away. Taking a molecule with i-j-k-l atoms, i-l interaction (1-4) is going to be calculated.
  • In the above example if we add in the [ pair ] section the i-l pair, then we are going to double count the interaction.
    -If we want to include i-l interaction in the pair list, in order to avoid double counting, we have to increase nrexcl=3
    Please correct me if there is any misconception.
6

Yes, you are correct. Also be aware, TraPPE-UA does not have any 1-4 interactions.

7

I’m fiddling with this right and I have a [ pairs ] directive set up because of different fudge parameters. Question is, where do I implement the different fudge LJ parameter? I see we can include a different fudge QQ by using the syntax below from the manual:

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

But what about the fudge LJ part?