From: Ropon-Palacios G. (biodano.geo_at_gmail.com)
Date: Thu Jan 28 2021 - 19:21:33 CST
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://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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