Hi Alexis,
The water-molecule_A LJ parameters are created using Lorentz-Berthelot rules: https://en.wikipedia.org/wiki/Combining_rules#Lorentz-Berthelot_rules
So, the water LJ parameters should remain unchanged (just use the MDL file from $AMBERHOME/dat/rism1d/mdl/). For molecule_A use the LJ parameters determined by your forcefield (remembering that LJSIGMA is r_min/2 in this case).
At this time, there is no way to do custom LJ parameters between different solvent sites.
Hope this helps,
Tyler
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‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐
On Sunday, January 16th, 2022 at 10:42 PM, Alexis Azucena <agazucena.up.edu.ph> wrote:
> Greetings,
>
> I have a water-molecule A cosolvent system for my 3D-RISM analysis. I
>
> already read the guidelines for creating the .mdl file for any cosolvents.
>
> In regards to LJ parameters, is it the nonbonded interactions of molecule A
>
> - molecule A or water - molecule A?
>
> Take note that I used molecule A since I cannot disclose the cosolvent that
>
> I am using. I hope for your assistance in this matter.
>
> Thank you.
>
> --
>
> Alexis G. Azucena, RChE
>
> Instructor
>
> School of Technology
>
> University of the Philippines Visayas
>
> *mobile: *+63917 584 1130 | +63918 214 1401
>
> *email: *agazucena.up.edu.ph
>
> AMBER mailing list
>
> AMBER.ambermd.org
>
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Jan 17 2022 - 11:30:03 PST
