From: McGuire, Kelly (mcg05004_at_byui.edu)
Date: Sat Mar 30 2019 - 14:20:18 CDT
Hey Brian, they have written a Python Wrapper to use TeraChem with NAMD for QMMMM. Link is below for anyone interested. That makes sense with passing around large sets of MM charges. Even if it's not close to 43x faster, even 2-3 times faster would be great.
http://www.ks.uiuc.edu/Research/qmmm/Scripts/run_terachem.py
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
________________________________
From: Brian Radak <brian.radak_at_gmail.com>
Sent: Saturday, March 30, 2019 1:13 PM
To: namd-l; McGuire, Kelly
Subject: Re: namd-l: TeraChem
This might have been discussed, but I don't know if this is planned in any official way - you are welcome to try scripting it.
It's also worth noting that fast QM codes do not always directly translate to fast QM/MM codes. Passing around a large set of MM charges (plus all of the ways that impacts the SCF calculation) can degrade performance in the range of 100-1000%. That's not to say it won't work, but it's not as guaranteed an outcome as you might assume.
On Fri, Mar 29, 2019, 7:31 PM McGuire, Kelly <mcg05004_at_byui.edu<mailto:mcg05004_at_byui.edu>> wrote:
Has anyone tried using TeraChem with NAMD for QMMM? They use GPUs, which some of their benchmarking showed 43x faster SCF calculations for about the same size QM region as I have. Anyone seen anything comparable to scalability with TeraChem and NAMD?
Kelly L. McGuire
PhD Candidate
Biophysics
Department of Physiology and Developmental Biology
Brigham Young University
LSB 3050
Provo, UT 84602
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