Hello Zoey,
The constant pH equations have been derived within a canonical ensemble. One would need to think if/how the equations would be affected in an NPT ensemble. This is why the error trap is in there.
Now to your questions: There would be no pressure control. All you would ensure is that the system is at one density compatible with the thermodynamic condition that you want, which for most purposes is all that you need.
I hope this helps,
Vinícius Wilian D. Cruzeiro, PhD
Postdoctoral Researcher
Department of Chemistry
Stanford University
Twitter: .vwcruzeiro
________________________________
From: Yang, Li-Yen via AMBER <amber.ambermd.org>
Sent: Friday, July 14, 2023 12:33 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: [AMBER] pressure control question
Dear Amber community,
I am trying to run a constant pH simulation on a protein complex.
I would like it to be run under the condition similar with my experiment which is 300K and 1atm.
At first, I tried to set my mdin file for my production run with both temperature control and pressure control so it can be NPT.
However, I got an error saying that Amber doesn’t support pressure control in ph constant explicit solvent simulation.
So now I am running my production run with NVT (by setting ntp=0 and ntb=1).
My question is:
1. If I run relaxation with constant pressure (1 atm) before my production run, will the production run (NVT) remain the pressure at around 1 atm?
1. If so, how do I check what the pressure is during the production run? (From my understanding, the PRESS from the output file is not the actual pressure from the system)
Thank you!
Best,
Zoey
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Received on Fri Jul 14 2023 - 14:00:02 PDT
