[gmx-users] correct rlist and Verlet scheme

Fri Feb 19 13:21:06 CET 2016

And here my hope for quick and  easy solution hath end.
All of the points you make ring true. Especially ones about software 
engineering and funding in science (or maybe I'm more familiar with them).

Actually, ne relatively recent paper, "Phosphorylation of PPARγ Affects 
the Collective Motions of the PPARγ-RXRα-DNA Complex" 
(http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123984#sec008), 
uses AMBER99SB-ILDN with GROMACS 4.6 and Justin Lemkul is listed as the 
first author. And the simulated structure is a protein-DNA complex. So 
it should be very close to my case.
The one thing that looks strange to me: both rvdw (LJ interacions) and 
box-solute distance set at 1.0 nm. Shouldn't the latter be larger to 
avoid probable periodic image interactions problems?
Otherwise, looks like my settings are generally the same, except 
forgetting that LINCS allows 2fs step.

17.02.2016 19:45, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
> Message: 4
> Date: Wed, 17 Feb 2016 13:45:46 +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:
> 	<CAMNuMARkUsmbzBRvNEie35aAhdwkPO-mGBEJEwXzgpUeEw67Xg at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> Yes, what you say is true, but very much "in short" and AFAIK true of all
> MD packages.:-)
>
> If e.g. AMBER (or anyone else) has a test suite for any force field, then
> we'll seriously consider implementing it, to e.g. verify before each
> release.:-)  IMO, defining such a suite is a research topic itself -
> particularly as the original parameterizations did so in the context of
> limitations in the methods of the day. If a force field was parameterized
> with a fixed buffer because nobody then knew how large a buffer was
> necessary for a given quality of relevant observable, it does not follow
> that the only possible acceptable practice now is to use that fixed buffer.
>
> Similar considerations apply to things like e.g. the use of long-ranged
> corrections for dispersion interactions. e.g. AMBER99 was parameterized
> without such corrections, so probably has built into its parameters some
> compensating errors, and any kind of validation-by-replication should in
> principle not use such corrections. But these days, I think that nobody
> would actually recommend parameterizing a force field without something
> like that, and experience suggests that using one is an improvement, even
> if though the change is not officially sanctioned anywhere that I know of.
> IMO showing that some range of force fields shows satisfactory agreement
> with experiment under certain .mdp setting combinations is useful evidence
> of an implementation that is valid, and that is what one can see in the
> literature.
>
> The state of the art in software engineering is that nobody much has time
> to test all the things that they'd like to test. (One large exception is
> software for control of devices that potentially affect human health.)
> Scientific software development has additional challenges because the
> people doing it are often lacking in formal training in best practice, and
> have to appear to publish science, in order to keep attracting funding, and
> this directly conflicts with spending time on good software engineering
> practice that granting and tenure committees will ignore later in their
> careers...
>
> Mark
>
> On Wed, Feb 17, 2016 at 1:01 PM Timofey Tyugashev<tyugashev at niboch.nsc.ru>
> wrote:
>
>> >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  ?????:
>>> > >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...
>>>>> > >> >--
>>>>> > >> >Gromacs Users mailing list
>>>>> > >> >
>>>>> > >> >* Please search the archive at
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>>>>> > >> >posting!
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>> >
>> >--
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