Re: Improve performance

From: Ming Sun (
Date: Mon Feb 15 2021 - 07:15:00 CST

Hi All,

A follow-up of previous discussion on the NAMD performed performances. I’m wondering if anyone has done benchmark on NAMD3 on AWS p2 instances or another GPU workstation? What would be an optimal / okay number of CPU per GPU ? I am using NAMD2.14 these days. I did not see improvements switching from 4-GPU machine to an 8-GPU machine while the number of CPU does not increase, at least at my hand

Any thoughts on NAMD3/ 2.14 are greatly appreciated.


From: "Vermaas, Josh" <<>>
Date: Thursday, January 28, 2021 at 7:45 PM
To: "<>" <<>>, "Ropon-Palacios G." <<>>
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.;!!DZ3fjg!t0qj3lFBcdvpNQmDX-ncJjXBjvRhCU6N3PxAox6tPJy255RhbwUZMj34czWhJwpQBA$ <;!!DZ3fjg!tjYMkz_rYz0-mcygjKo9GeKdRm_0FZD8S4mIIgeJcpPHpSrKAvJF-wFdVk0GayNq_w$>


From: <<>> on behalf of "Ropon-Palacios G." <<>>
Reply-To: "<>" <<>>, "Ropon-Palacios G." <<>>
Date: Thursday, January 28, 2021 at 7:18 PM
To: "<>" <<>>
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?





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