Dear AMBER Community,
I am currently working on a simulation involving a membrane-embedded
protein-ligand system. Typically, for such systems, I used the following
settings:
- barostat = 2
- ntp = 3
- csurften = 3
- gamma_ten = 0.0
- ninterface = 2
However, I have encountered an issue when trying to calculate the relative
binding free energy of the protein-ligand system using the '*ifsc*' option.
The 'ifsc' option only supports ntp=1, which conflicts with my usual
settings for membrane-embedded systems.
Given this constraint, I am seeking advice on whether it is acceptable to
run the simulation with ntp=1 for a membrane-embedded protein-ligand system.
Are there any potential issues or considerations I should be aware of when
using this setting?
Any insights or recommendations from those with experience in similar
simulations would be greatly appreciated.
Thank you for your assistance.
Best regards,
Jinyoung
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Received on Mon Jun 17 2024 - 03:30:02 PDT
