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 - 01:30:02 PDT
