[gmx-users] Setting correct non-bonded and pair (LJ) parameters in ffnonbonded.itp

[Apramita Chand]

Dear All,
In my previous posts, I had written about errors arising upon changing the
combination rule and using sigma and epsilon values. Dr Lemkul was kind
enough to point out that incorrect formatting of the ffnonbonded.itp might
cause errors and that the [nonbond params] as well as [pairtypes] section
need to be supplied with the parameters.
I have some doubts regarding the calculations of the [nonbond params] and
particularly the [pairstype] section. I have gone through the archives and
it has certainly helped me to understand the logic better but still some
doubts persist as below
1.  As per manual, The combination rule 1 states that geometric mean of C6
and C12 of (respective atomtypes section) of two atoms should give C6ij and
C12ij which is included in the [nonbond params] section. In ffnonbonded.itp
of gromos53a6ff, I see that C12(OM)=7.4149321e-07 and C12(O)=1e-06 give
C12(OM O)= 8.611e-07. But when I calculate C12 (OA O), using
C12(OA)=1.505529e-06 and C12(O)=1e-06, I get the value C12=1.227e-06 while
the C12 mentioned for OA O interactions in the itp file =1.38651e-06.
The interaction parameters C6ij and C1ij in most other cases also don't
match with the geometric mean rule.
What could be the reason for such discrepancy? I have already run
simulations trusting this ffnonbonded.itp file to be correct (using
combination 1). Are those wrong?

2.  What is the formula for calculation of [pairtypes] section in the
ffnonbonded.itp? I haven't found any concrete answers yet to this doubt
yet.



I'm hoping once I am clear about how the calculations for C6ij and C12ij
for [nonbond params] and [pairtypes] sections have been done, I will be
able to calculate the same using sigma and epsilon values for combinations
2 and 3 as Justin has suggested.
Looking forward to your help,
Thanking you,
Yours sincerely,
Apramita Chand