Hello, Amber users!
Recently, I want to empoly Amber program packages to simulate a protein in water system in order to guide my wet experiments. I plan to use the cuda-version of Amber18 to run. But I had mentioned some tips from amber18 manual that was "Avoid using the NPT ensemble (ntb=2) when it is not required; if needed make use of the Monte Carlo barostat (barostat=2). Performance will generally be NVE>NVT>NPT (NVT~NPT for barostat=2)." In my knowledges, the protein-salt-water system was should be considered to simulate under the npt ensemble for final MD production. So, I'm confused whether to chose the option ntb=1 or ntb=2. I known that the protein-salt-water simualtion should be equilibrated by NVT and NPT ensemble before MD production. So, How should I process the simulation with amber18 cuda version. Please help me. Any suggestion is welcome.
Best wishes!
Ning Wang
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Received on Tue Sep 01 2020 - 00:00:02 PDT
