On Sun, Jul 06, 2025, Zihao Bai wrote:
>
>I am doing TI between MM and QM/MM (as in this paper,
>DOI: 10.1021/acs.jctc.6b01217). I noticed that TI appears to be
>incompatible with the Monte Carlo barostat in Sander.
>
>Given that the Berendsen barostat may lead to problematic
>virial and density values (it seems also reported by others:
>http://archive.ambermd.org/201212/0011.html ), I was wondering if you have
>any suggestions or recommended alternatives to address this?
One, perhaps possible, idea: equilibrate the density using MM only, then run
QM/MM in NVT. You would need to decide if you really need volume
fluctuations during the QM part of the simulation.
....dac
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Received on Mon Jul 07 2025 - 15:00:02 PDT
