From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Feb 02 2021 - 18:31:51 CST
Unfortunately, most of the enhanced sampling methods in NAMD, including the ones you mention, do not yet work for the GPU-resident integrator. We are still working on porting features to the GPU.
-- David J. Hardy, Ph.D. Beckman Institute University of Illinois at Urbana-Champaign 405 N. Mathews Ave., Urbana, IL 61801 dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/ > On Jan 28, 2021, at 7:21 PM, Ropon-Palacios G. <biodano.geo_at_gmail.com> wrote: > > Dear Josh, > > Namd3 have implement umbrella sampling, colvar, and smd protocols ? > > Geo. > > From: "Vermaas, Josh" <vermaasj_at_msu.edu> > Date: Thursday, January 28, 2021 at 7:45 PM > To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo_at_gmail.com> > Subject: Re: namd-l: Improve performance > > For the best NAMD performance on a GPU, use NAMD 3. This blog from NVIDIA has been my goto for explaining the differences to folks that haven’t used NAMD 3 yet. https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/ <https://urldefense.com/v3/__https://developer.nvidia.com/blog/delivering-up-to-9x-throughput-with-namd-v3-and-a100-gpu/__;!!DZ3fjg!tjYMkz_rYz0-mcygjKo9GeKdRm_0FZD8S4mIIgeJcpPHpSrKAvJF-wFdVk0GayNq_w$> > > -Josh > > From: <owner-namd-l_at_ks.uiuc.edu> on behalf of "Ropon-Palacios G." <biodano.geo_at_gmail.com> > Reply-To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo_at_gmail.com> > Date: Thursday, January 28, 2021 at 7:18 PM > To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu> > Subject: namd-l: Improve performance > > Dear namd users, > > How can i improve namd2.14 performance on GPU? > > I`m using namd2.14 for run membrane protein simulation, but namd only use nor more the 50% of GPU, as can I make to improve this performance. > > For other hand, if during equilibration of protein-membrane is necessary keep water out membrane? > > Thanks, > > Best, > > Geo.
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