[AMBER] Advice on Simulated Annealing

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Wed, 29 Dec 2021 13:39:23 -0500

Dear Amber Community,

I’m wondering if advice can be offered on how to select the maximum temperature and heating/cooling schedules for simulated annealing.
I’m thinking of using simulated annealing for the below purpose; if a different approach seems more appropriate, I’d appreciate those suggestions as well.

I have an AlphaFold-predicted protein into which several porphyrin-type cofactors were inserted. The geometry of the system is much improved after minimization, but some backbone motion is still needed to alleviate the strain between two of the porphyrin rings (e.g. one ring is very buckled to accommodate the substituent on the other perpendicular porphyrin ring).
Ultimately, I want to compute redox potentials at the QM/MM level, so I want to make sure the geometry is as good as possible. What are some ways I can improve my starting structure?


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Received on Wed Dec 29 2021 - 11:00:02 PST
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