[gmx-users] Is amber ff compatible with user-specified potential functions?

Du, Yu duyu at sioc.ac.cn
Sat Sep 23 13:16:10 CEST 2017

Dear GMX users, 

The context of my question is that I want to simulate the interaction between protein and ligand with Weeks-Chandler-Andersen (WCA), and normal LJ12-6 potential for others. 
mdp file like this
energygrps = Protein Ligand, energygrp-table= Protein Ligand
So I need the two xvg files: table.xvg, table_Protein_Ligand.xvg.

Context end 

I'm trying the WCA nbfunc and the main reference is the User Specied non-bonded potentials in
gromacs. This webpage and attached pdf is 7 years old. It said that "If you specify your own potentials these parameters must be both set equal to 1 (nbfunc and comb-rule)."

I'm using gromacs 2016.3 version, has this both-to-be-1 condition be changed and been more flexible?

And I'm asking that if I use WCA potential and amber ff whose the nbfunc and comb-rule is 1 and 2, will this conflict with the both-to-be-1 condition? If so, how can I work around this?



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