[gmx-users] correct rlist and Verlet scheme

[Timofey Tyugashev]

In short, FFs were tested to some degree when they were added in GROMACS 
to reproduce AMBER results, but there is no certainty if they actually 
do this now and 'correct' mdp settings to run them are unknown. For any 
of the versions that are listed in GROMACS.
Is that correct, or I'm missing something in translation?

16.02.2016 18:03, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> Message: 2
> Date: Tue, 16 Feb 2016 11:23:06 +0000
> From: Mark Abraham<mark.j.abraham at gmail.com>
> To:gmx-users at gromacs.org,gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue
> 	76
> Message-ID:
> 	<CAMNuMASUTdHR8sOt1qt4XdCzOgsDJSfGo8umiUhrpffxXfAagg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> The ports of all the AMBER force fields were all tested to reproduce AMBER
> when when they were added to GROMACS. Many of our regressiontests use those
> force fields, so there is reason to expect that they all continue to work.
> The Verlet scheme is tested to implement what the documentation says it
> does. There have been bugs introduced (and fixed) in how GROMACS
> preprocessing tools implement the requirements of AMBER force fields,
> including ILDN.
>
> To be able to say "this force field is tested to work correctly with this
> cutoff scheme in this version of GROMACS" requires the community to agree
> on what that means, e.g. a large collection of single-point energies+forces
> agree to within a certain precision, and simulations done in a particular
> model physics produce these ensembles with these observables, etc. That
> hasn't happened yet. As far as I know, the ability of the different AMBER
> code versions to correctly continue to implement all the AMBER force fields
> has a similar kind of question mark over it. Just having the same name is
> not enough;-)
>
> Mark
>
> On Tue, Feb 16, 2016 at 11:17 AM Timofey Tyugashev<tyugashev at niboch.nsc.ru>
> wrote:
>
>> >So, are there any other Amber force fields more suitable and more tested
>> >for GROMACS?
>> >
>> >15.02.2016 21:00,gromacs.org_gmx-users-request at maillist.sys.kth.se  ?????:
>>> > >Message: 1
>>> > >Date: Mon, 15 Feb 2016 13:15:02 +0000
>>> > >From: Mark Abraham<mark.j.abraham at gmail.com>
>>> > >To:gmx-users at gromacs.org,gromacs.org_gmx-users at maillist.sys.kth.se
>>> > >Subject: Re: [gmx-users] correct rlist and Verlet scheme
>>> > >Message-ID:
>>> > >       <
>> >CAMNuMATMbmGvbfJ49ez+4K_BftDmkyFYiw5iZ-EECwiCUJBLuQ at mail.gmail.com>
>>> > >Content-Type: text/plain; charset=UTF-8
>>> > >
>>> > >Hi,
>>> > >
>>> > >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev<
>> >tyugashev at niboch.nsc.ru>
>>> > >wrote:
>>> > >
>>>>> > >> >I've studied the relevant sections of the manual, but I don't consider
>>>>> > >> >myself to be familiar enough with this field to successfully guess the
>>>>> > >> >right settings.
>>>>> > >> >
>>>>> > >> >ff99sb-ildn is included in the gromacs distribution, so shouldn?t be
>>>>> > >> >there some recommended settings for it?
>>> > >Ideally, yes. But nobody has made a particular effort for that
>> >combination.
>>> > >
>>> > >Or else how was it tested to run
>>>>> > >> >properly?
>>>>> > >> >
>>> > >In principle, one would have to e.g. show that
>>> > >https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970904/   can be
>> >replicated.
>>> > >That's not a straightforward proposition...
>> >--
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