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

[Du, Yu]

Dear GMX users, 

After several tests, I found that Verlet (2016.3 version) still don't support the vwdtype=user with tabulated potentials:

ERROR 1 [file md.mdp]:
  With Verlet lists only cut-off and PME LJ interactions are supported

So with Verlet on, are there any decent ways to turn off the attractive part of the vwd potential?

Thanks for your advice. 

Yu


> -----Original Messages-----
> From: "Du, Yu" <duyu at sioc.ac.cn>
> Sent Time: 2017-09-23 19:15:52 (Saturday)
> To: gmx-users at gromacs.org, gromacs.org_gmx-users at maillist.sys.kth.se
> Cc: 
> Subject: [gmx-users] Is amber ff compatible with user-specified potential functions?
> 
> 
> 
> 
> 
> 
> 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?
> 
> 
> 
> 
> Thanks.
> 
> 
> Yu
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