I'm not sure if I'm missing something, but there may be an issue with the use of the 12-6-4 terms with multiple ion types.
When I try to add the C4 term for multiple ions, the term for the first ion seems to be overwritten when I add the second.
My parmed input:
parm en.prmtop
setOverwrite True
add12_6_4 .%Ni2+
printljmatrix :1
add12_6_4 .%Cl-
printljmatrix :1
outparm en.prmtop
and the relevant portions of the Lennard Jones matrix (for the first and second print steps):
n3 [1] Ni2+ [5] 85192.212900 143.259667 442.105263 3.255000 0.060227
n3 [1] Cl- [6] 4619547.710000 2345.644950 0.000000 3.974000 0.297759
c3 [2] Ni2+ [5] 92783.171500 133.906203 156.357895 3.339000 0.048314
c3 [2] Cl- [6] 4763145.150000 2133.298140 0.000000 4.058000 0.238863
hn [3] Ni2+ [5] 90.163847 2.569229 57.031579 2.031000 0.018303
hn [3] Cl- [6] 16927.109200 78.273838 0.000000 2.750000 0.090488
h1 [4] Ni2+ [5] 4589.921050 18.331132 57.031579 2.818000 0.018303
h1 [4] Cl- [6] 346905.501000 354.348684 0.000000 3.537000 0.090488
n3 [1] Ni2+ [5] 85192.212900 143.259667 0.000000 3.255000 0.060227
n3 [1] Cl- [6] 4619547.710000 2345.644950 -78.947368 3.974000 0.297759
c3 [2] Ni2+ [5] 92783.171500 133.906203 0.000000 3.339000 0.048314
c3 [2] Cl- [6] 4763145.150000 2133.298140 -27.921053 4.058000 0.238863
hn [3] Ni2+ [5] 90.163847 2.569229 0.000000 2.031000 0.018303
hn [3] Cl- [6] 16927.109200 78.273838 -10.184211 2.750000 0.090488
h1 [4] Ni2+ [5] 4589.921050 18.331132 0.000000 2.818000 0.018303
h1 [4] Cl- [6] 346905.501000 354.348684 -10.184211 3.537000 0.090488
I apologize if that is hard to read.
The important part is the third column (which includes the r^-4 coefficient).
For Nickel ions, the C4 coefficient is added properly to all interactions in the first step.
In the second step, it is added to all chlorine ions, BUT the Nickel C4 coefficients are overwritten with zeroes.
Is there a way to add the C4 term to all relevant ions?
If I am wrong (which I would love to be) and there is something I missed, please let me know.
Thanks,
Anthony Seitz
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Received on Fri Mar 09 2018 - 11:30:01 PST
