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bugs and the GPU code which you really want is way out of date.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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Received on Tue Jul 16 2019 - 13:00:03 PDT
