Re: NAMD How to calculate ns/day

From: Abhishek TYAGI (
Date: Thu Dec 08 2016 - 01:38:04 CST

You have to provide the config file to run your simulations, please check the tutorial, it clearly state how to use the config file.

The easy way to make namd work is to copy the binaries of namd to usr/local/bin/ and to the library usr/local/lib/ .



Abhishek Tyagi

PhD Student

Chemical and Biomolecular Engineering

Hong Kong University of Science and Technology

Clear Water Bay, Hong Kong

From: <> on behalf of Shikha Sharma <>
Sent: Thursday, December 8, 2016 1:01:44 PM
To:; Ajasja Ljubetič
Subject: Re: namd-l: NAMD How to calculate ns/day

Good morning,

I am installing NAMD on ubuntu facing difficulty in the step "Set up build directory and compile"

./config Linux-x86_64-g++ --charm-arch net-linux-x86_64 This command is showing error that ./config is not present

please suggest how i can correct this error

On Thu, Dec 8, 2016 at 4:29 AM, Ajasja Ljubetič <<>> wrote:

Probably if you increase the number of steps, the difference will decrease. NAMD has some startup cost (parsing all the files etc...). What was the absolute wall time? If it was less than about 100 s I would not trust the results.


On 7 December 2016 at 23:02, Jan Fredin <<>> wrote:
I am running the ApoA1 benchmark using 10,000 time steps and outputtiming=100 with all the other input from the standard benchmark apoa1.namd file. I'm running on a single node of Xeon Haswell with P100 GPUs. I am interested in the ns/day and thought 10,000 time steps would be enough to have the WallClock time be usable in the ns/day calculation. I found that taking the reciprocal of the average of the 6 Benchmark time lines day/ns gave 26.3 ns/day but the straight calculation of ns simulated (0.01 ns) and WallClock time (XX sec / 86400 sec/day) gave only 14.3 ns/day.

What work contributing to the WallClock time is not being included in the Benchmark time lines?
Under what circumstances do the 2 methods of calculating ns/day converge to the same value?


Dr. Jan Fredin
SGI, Sr. Applications Engineer - Lead
Austin, TX

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