[gmx-users] correct rlist and Verlet scheme

Fri Feb 19 14:51:31 CET 2016

On Fri, Feb 19, 2016 at 1:23 PM, Timofey Tyugashev <tyugashev at niboch.nsc.ru>
wrote:

> 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.
>

I guess you meant 4-5 fs *if* combined with virtual sites. At 2 fs you can
use h-bond only constraints if i) you prefer the resulting physics or ii)
you want to have a bit better performance and a lot better scalability.

>
>
> 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
>>>>>> > >> >http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List
>>>>>>  before
>>>>>> > >> >posting!
>>>>>> > >> >
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>>>>>> > >> >
>>>>>> > >> >* For (un)subscribe requests visit
>>>>>> > >> >
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>>>>>>  or
>>>>>> > >> >send a mailtogmx-users-request at gromacs.org.
>>>>>>
>>>>> >
>>> >--
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