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

[David van der Spoel]

On 23/09/17 16:58, Du, Yu wrote:
> 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?
> 
You can not use User potentials with the Verlet scheme yet.


> 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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-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se