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

From: Pengfei Li <ambermailpengfei.gmail.com>
Date: Mon, 19 Mar 2018 18:03:36 -0500

Hi Anthony,

Jason is right. For adding the C4 terms for multiple ion types, you need to specify them with one single add12_6_4 command, as specified in the Usage term 1 of the add12_6_4 command in the Page 253 of the AMBER 2017 manual: http://ambermd.org/doc12/Amber17.pdf <http://ambermd.org/doc12/Amber17.pdf>.

Kind regards,
Pengfei

> On Mar 18, 2018, at 5:07 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
> On Fri, Mar 9, 2018 at 2:28 PM, Seitz, Anthony Joseph <seitzant.msu.edu <mailto: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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <http://lists.ambermd.org/mailman/listinfo/amber>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 19 2018 - 16:30:03 PDT
Custom Search