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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jun 18 2025 - 10:00:02 PDT
