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

[Du, Yu]

Dear GMX users, 

Hope you can see this email. 
Thanks for your help.

Yu


> -----Original Messages-----
> From: "Du, Yu" <duyu at sioc.ac.cn>
> Sent Time: 2017-09-23 22:58:29 (Saturday)
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Cc: duyu at sioc.ac.cn
> Subject: Re: [gmx-users] Is amber ff compatible with user-specified potential functions?
> 
> 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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