Note the second protocol is implemented in the following script:
https://github.com/drroe/AmberMdPrep
-Dan
On Fri, Oct 10, 2025 at 4:31 AM Téletchéa Stéphane via AMBER <
amber.ambermd.org> wrote:
> Le 10/10/2025 à 09:15, Surabhi Singh 24933024 via AMBER a écrit :
> > I am working on protein-DNA complex, and while doing equilibration I'm
> > getting vlimit error...
> Dear Surabhi,
>
> This error means probably there is some (little) weirdness in your input
> file,
> but it also come from the fact that in some situations (GPU) vlimit is
> not limited to 20,
> as indicated by the manual, but set to -1 (thus unlimited).
>
> Add vlimit=20 to your input file (which is a far reasonable value
> indicated in the manual),
> and the problem should disappear. If not check your protocol, and/or use
> the one from
> the BCS consortium:
>
> - Ivani, I., Dans, P., Noy, A. et al. Parmbsc1: a refined force field
> for DNA simulations.
> Nat Methods 13, 55–58 (2016). https://www.doi./10.1038/nmeth.3658
>
> or the one by Daniel Roe and Brooks:
>
> - Daniel R. Roe, Bernard R. Brooks; A protocol for preparing explicitly
> solvated systems for stable molecular dynamics simulations.
> J. Chem. Phys. 7 August 2020; 153 (5): 054123.
> https://doi.org/10.1063/5.0013849
>
> These should solve your issues.
>
> If you want to keep your existing protocol, double check the timestep
> during the heating steps (1fs, and not 2fs).
>
> HTH,
>
> Stéphane
>
> --
> Maître de conférences Hors Classe, PEDR, HDR
> US2B, Nantes Université, CNRS, UMR 6286, Team Structural Bioinformatics,
> F-44000 Nantes
> http://www.us2b.univ-nantes.fr/ - http://www.steletch.org
>
>
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Received on Fri Oct 10 2025 - 10:00:02 PDT
