Hi,
A short follow-up to confirm that umbrella sampling does work with adQM/MM. The DUMPAVE file was eventually generated in my simulations, though with a significant delay.
Upon closer inspection, ions like O⁻ and OH⁻ formed dynamically (and were diffusing a lot). This likely caused the analytical solution to take longer to converge (hence the delay in dumpave file generation), before the simulations crashed eventually.
Best,
Ameni
________________________________
De : Goetz, Andreas <awgoetz.ucsd.edu>
Envoyé : jeudi 26 juin 2025 19:45:41
À : Ameni BEN ABDELJAOUED; AMBER Mailing List
Objet : Re: [AMBER] Issue with dumpave in adaptive solvent QM/MM umbrella sampling
Hi Ameni,
Can you confirm your setup works as expected for regular MD? In principle it should work with adaptive solvent QM/MM simulations.
All the best,
Andy
—
Dr. Andreas W. Goetz
Associate Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
On Jun 26, 2025, at 9:20 AM, Ameni BEN ABDELJAOUED via AMBER <amber.ambermd.org> wrote:
Dear Amber developers and users,
I’m currently running adaptive solvent QM/MM simulations within an umbrella sampling protocol. Despite specifying the DUMPAVE file, it is not being generated. As a result, I’m forced to write the trajectory at every frame in order to extract the necessary data afterward.
This approach is not optimal, especially given my limited storage capacity.
Is this expected behavior? Are there more efficient alternatives to avoid writing full trajectories at every step?
Thank you in advance for your help.
Best regards,
Ameni B.A
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Received on Sat Jun 28 2025 - 01:30:02 PDT
