[gmx-users] correct rlist and Verlet scheme

Wed Feb 17 18:07:30 CET 2016

Hi,

The short-range interaction treatment in AMBER and GROMACS is quite
different (to the best of my knowledge), so obsessing about rlist
seems pointless to me.

AMBER uses a heuristic list update where search is triggered based
particles tracking ("safe" but inefficient strategy), whereas GROMACS
uses a fixed list update frequency. The automated buffer estimate that
ensures control of the non-boneded drift. Without controlling _both_
buffer and search frequency (and a bunch of other subtle
implementation details) you won't achieve identical computation.

Hence, if you want to have (more or less) the same non-bonded
calculation implemented in GROMACS, strictly speaking you'd have to
use nstlist=1 or if you accept to be a bit less strict, a huge manual
buffer (and small-ish nstlist) should achieve more or less the same.
However, there are plenty of other algorithmic and implementation
differences between AMBER and GROMACS, so I don't think it's worth
worrying about getting the Verlet list buffer length to match.

Cheers,
--
Szilárd

PS: I thought AMBER FF was parametrized with 0.9 nm cut-off, isn't it?

On Wed, Feb 17, 2016 at 2:45 PM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 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 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...
>> >> >--
>> >> >Gromacs Users mailing list
>> >> >
>> >> >* Please search the archive at
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>> >> >posting!
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