Dear Amber community,
For my PhD project, I need to do MD simulations of protein crystals. I found your tutorial where it is recommended to use at least 2 Unit Cells. But in the paper by Cerutti et al., (2010, ACS, Simulations of a Protein Crystal with a High Resolution X-ray Structure: Evaluation of Force Fields and Water Models), to which the tutorial refers, 12 unit cells were used.
I am analyzing two different proteins with about 130 residues forming a unit cell of six and eight asymmetric units, respectively. Using 12 unit cells seems to be too computationally expensive, leading to my question:
What is the "right" number of unit cells for simulating protein crystals? Is there a rule of thumb?
Thank you in advance!
With best regards,
Thorben
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Received on Tue Nov 08 2022 - 06:30:03 PST
