Cholesterol is not required – I don’t know any impact, if any, on the buckling of large membrane patches.
Best,
Callum
From: Cherry, Kendall via AMBER <amber.ambermd.org>
Date: Thursday, June 19, 2025 at 11:21
To: Dickson, Callum <callum.dickson.merck.com>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Recommended barostat for membrane protein simulations?
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Hi Callum,
Thank you very much for the thorough response. I’ll look at that paper.
Regarding the simulation setup, is cholesterol required or just helpful to prevent buckling? All of our lab’s previous simulations and experiments have been run without cholesterol, so I’d prefer to not stray too far from our current setup.
Best,
Kendall Cherry
From: Dickson, Callum <callum.dickson.merck.com>
Date: Wednesday, June 18, 2025 at 7:01 PM
To: Cherry, Kendall <kche.email.unc.edu>, AMBER Mailing List <amber.ambermd.org>
Subject: Re: Recommended barostat for membrane protein simulations?
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Hi Kendall,
The paper to look at on this would be this one: https://onlinelibrary.wiley.com/doi/10.1002/jcc.26798
With large membrane patches, the MC barostat can cause buckling. With smaller patches, the area per lipid is decreased (bilayer condenses somewhat) which as you say was also covered in the Lipid21 paper. With a LJ force-switch (which is available in Amber) this behaviour can be corrected, although I have not managed to test this myself.
In general, I have not seen issues using the MC barostat for regular membrane protein systems, typically using POPC and a small fraction of cholesterol (vdW cut-off 10 A but no force-switch). If you see the bilayer condensing too far you could try the LJ force-switch.
Best,
Callum
From: Cherry, Kendall via AMBER <amber.ambermd.org>
Date: Wednesday, June 18, 2025 at 12:54
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Recommended barostat for membrane protein simulations?
EXTERNAL EMAIL– Use caution with any links or file attachments.
Hello Amber community,
I am running simulations of membrane proteins and am curious what barostat would be recommended. I plan to run semi-isotropic pressure scaling (ntp = 3). I have been told that Berendsen isn’t necessarily recommended due to the poor quality of its ensemble representation. However, I saw this in the Lipid21 paper:
“All production simulations used the Berendsen barostat for pressure coupling. (24) We also ran single exploratory simulations of 300 ns per lipid type using the Monte Carlo barostat, (29) which allows a speed-up in simulation throughput, keeping all other simulation settings identical. As shown in Table S1<
https://pubs.acs.org/doi/suppl/10.1021/acs.jctc.1c01217/suppl_file/ct1c01217_si_001.pdf>, we find that areas per lipid are depressed for all lipid types, dropping by an average of 3.78 Å2. We therefore recommend the Berendsen barostat pressure coupling for lipid bilayer simulations in AMBER.”
I think there will have to be a trade-off between accurately modeling the protein and the lipids, if I understand these barostats correctly. I am most concerned with modeling the protein accurately; if this is the case, should I go with the Monte Carlo barostat?
Any advice would be welcomed.
Thank you,
Kendall Cherry
Chemistry PhD Student
University of North Carolina at Chapel Hill
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Received on Thu Jun 19 2025 - 10:30:02 PDT
