Hi Katie,
No, this is not what I meant. Only sander can run QM/MM simulations, not pmemd (or pmemd.cuda). sander does not run on GPUs. It has built-in QM methods but can also use several external QM programs including TeraChem which runs on GPUs.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<http://www.awgoetz.de>
On Jul 3, 2018, at 1:07 PM, Witkin, Katharine R <katharine-corum.uiowa.edu<mailto:katharine-corum.uiowa.edu>> wrote:
Hi Andy, I'm a bit confused. Are you saying, I can use a program called TeraChem to perform the QM portion of my QM/MM calculation. They can I use pmemd.cuda to perform the MM portion? And somehow they work together?
Thanks,
Katie
________________________________
From: Goetz, Andreas <agoetz.sdsc.edu<mailto:agoetz.sdsc.edu>>
Sent: Tuesday, July 3, 2018 3:05:01 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER: QM/MM calculations using GPU
Hi Katie,
Only sander supports QM/MM. You can use GPUs for the QM portion of a QM/MM simulation with a GPU enabled QM code. Currently we have an interface to TeraChem.
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu<mailto:agoetz.sdsc.edu><mailto:agoetz.sdsc.edu>
Web: www.awgoetz.de<http://www.awgoetz.de><http://www.awgoetz.de>
On Jul 3, 2018, at 12:52 PM, Witkin, Katharine R <katharine-corum.uiowa.edu<mailto:katharine-corum.uiowa.edu><mailto:katharine-corum.uiowa.edu>> wrote:
Hi, I would like to run QM/MM and possibly QM/MM MD simulations using our GPU system. AMBER16 is installed and works great, I have performed MD simulations on it. Next I was going to move onto QM/MM calculations, I have been going through the manual to learn more about pmemd.cuda and the archived emails. Now I am under the impression that I cannot use AMBER16 on my GPU to run QM/MM.
Can I use my GPU system to run QM/MM or QM/MM MD simulations?
Thanks,
Katie
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Received on Tue Jul 03 2018 - 15:00:03 PDT
