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-requ...@maillist.sys.kth.se пишет:
Message: 2
Date: Tue, 16 Feb 2016 11:23:06 +0000
From: Mark Abraham<mark.j.abra...@gmail.com>
To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue
76
Message-ID:
<camnumasutdhr8sot1qt4xdczogsdjsfgo8umiuhrpffxxfa...@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<tyugas...@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-requ...@maillist.sys.kth.se ?????:
> >Message: 1
> >Date: Mon, 15 Feb 2016 13:15:02 +0000
> >From: Mark Abraham<mark.j.abra...@gmail.com>
> >To:gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se
> >Subject: Re: [gmx-users] correct rlist and Verlet scheme
> >Message-ID:
> > <
>camnumatmbmgvbfj49ez+4k_bftdmkyfyiw5iz-eecwicujb...@mail.gmail.com>
> >Content-Type: text/plain; charset=UTF-8
> >
> >Hi,
> >
> >On Mon, Feb 15, 2016 at 12:17 PM Timofey Tyugashev<
>tyugas...@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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