Dear all,
thank you so much for your valuable suggestions.
Alessandro
Il giorno mar 16 lug 2019 alle ore 21:30 David Cerutti <dscerutti.gmail.com>
ha scritto:
> Dear Alessandro,
>
> As Matias mentioned, AT19 is free (AmberTools has been GPL for the past few
> years), and if your version is "quite old" (pre 14) then there are likely
> bugs and the GPU code which you really want is way out of date. If you are
> using something earlier than 12, you may not be working with the GPU code
> at all. Modern GPUs are 300-400x more powerful than optimized code running
> on a single CPU core, so well worth the electricity and human time to take
> advantage of our workhorse engine.
>
> As for the polarizable force field, the thing really hobbling them is the
> lack of implementation on GPU accelerators. Four to ten times higher
> computational cost compounded with CPU code. But we may be reaching the
> limits of accuracy in fixed-charge models (it's now taking us milliseconds
> of simulation time to compare relative secondary structure propensities in
> different candidates), so anything that can show better behavior on shorter
> timescale phenomena could pull ahead.
>
> Dave
>
>
> On Tue, Jul 16, 2019 at 11:53 AM Matias Machado <mmachado.pasteur.edu.uy>
> wrote:
>
> > Dear Alessandro,
> >
> > Notice, you can get the new version of AMBER Tools (19) free for
> academics
> > from the website.
> >
> > You can check the following paper for an update on DNA force fields:
> >
> > # How accurate are accurate force-fields for B-DNA? NAR, 2017 [
> > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397185]
> >
> > From which I would say parmbsc1 or OL15 are very good choices (both
> > already implemented in AMBER since AMBER Tools 16). I prefer the former
> > parameter set but it's a matter of taste... however, both force fields
> > should run OK on older version of the code...
> >
> > I'm not familiar in using polarizable force fields, but there seems to be
> > recent developments [https://doi.org/10.1021/acs.jctc.7b00067] (top
> > result in a google search)
> >
> > Best,
> >
> > Matias
> >
> >
> > ----- Mensaje original -----
> > De: "Alessandro LANDI" <alelandi1.unisa.it>
> > Para: "AMBER Mailing List" <amber.ambermd.org>
> > Enviados: Martes, 16 de Julio 2019 8:11:14
> > Asunto: [AMBER] Recent Force Fields for nucleotides
> >
> > Dear all,
> > I am currently performing molecular dynamics simulations on DNA single
> and
> > double strands in water. Unfortunately, I am using a quite old version of
> > both Amber and AmberTools suite, therefore I am considering buying the
> > latest version.
> >
> > However, as a newbie, I would like to get information about the most
> > up-to-date force field to be used for the DNA and, in particular, if
> there
> > are any polarizable force fields to be used when simulating DNA
> sequences.
> > I have read about some recent force fields (e.g. ff12pol, even though, to
> > the best of my knowledge, it has not been yet implemented in Amber18),
> but
> > I have not been able to understand if they could be used only for
> peptydes,
> > or if some of them has been parametrized also for DNA.
> >
> > Can you please provide me some information about the available force
> fields
> > for DNA in Amber18 and if they are polarizable?
> >
> > Thanks in advance,
> > Alessandro
> >
> > --
> > Alessandro Landi, Ph.D. Student
> > Dipartimento di Chimica e Biologia "Adolfo Zambelli"
> > Università degli Studi di Salerno
> > Via Giovanni Paolo II, 132 - 84084 - Fisciano (SA)
> > Phone number 089969390
> >
> > <
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--
Alessandro Landi, Ph.D. Student
Dipartimento di Chimica e Biologia "Adolfo Zambelli"
Università degli Studi di Salerno
Via Giovanni Paolo II, 132 - 84084 - Fisciano (SA)
Phone number 089969390
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Received on Wed Jul 17 2019 - 02:30:03 PDT
