Re: [AMBER] Lennard Jones 12-6-4 with Multiple Ion Types

From: Jason Swails <jason.swails.gmail.com>
Date: Sun, 18 Mar 2018 18:07:13 -0400

On Fri, Mar 9, 2018 at 2:28 PM, Seitz, Anthony Joseph <seitzant.msu.edu>
wrote:

> 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.
>

‚ÄčThis certainly looks weird, and should probably not happen (that is,
throwing away 12-6-4 parameters). However, it's better to assign them to
all of the ions you want at once, like this:

parm en.prmtop
setOverwrite True
add12_6_4 .%Ni2+,Cl-‚Äč
printLJMatrix :1
outparm en.prmtop

HTH,
Jason

-- 
Jason M. Swails
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Received on Sun Mar 18 2018 - 15:30:02 PDT
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