From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Fri Jun 24 2022 - 10:28:19 CDT
Hi Gerald,
For plain NVT (using Langevin thermostat) and NPT (adding Langevin piston), the most recent NAMD 3.0alpha12 release should work well for you. We have fixed a few bugs since the alpha 10 and 11 releases. The bugs were not related to the numerics, which has been stable since early alpha releases.
Please see the NAMD 3.0 alpha release page for details. Some things considered routine are still problematic, like combining minimization with GPU-resident dynamics in the same run.
Best regards,
Dave
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_illinois.edu <mailto:dhardy_at_illinois.edu>, http://www.ks.uiuc.edu/~dhardy/ <http://www.ks.uiuc.edu/~dhardy/> > On May 17, 2022, at 10:18 AM, Gerald Keller <gerald.keller_at_uni-wuerzburg.de> wrote: > > Hi there, > > in our group we are considering to switch from NAMD 2.14 to NAMD 3-alpha10. Our main application is to run plain NVT and NPT MD simulations of protein-ligand-complexes or membrane-protein-systems in explicit solvent. Since the latest version is alpha10, we wanted to ask if this is still a ‘real’ alpha-version and to what extent could one expect (numeric) instabilities or bugs? Or in other words: Can we use NAMD 3-alpha without hesitation for plain NVT and NPT MD simulations in explicit solvent? > > Best regards, > Gerald
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