Hello,
I want to confirm that I am doing this correctly. I want to see the transfer of a proton from one substrate to an oxy-ferryl group on a heme. I would like to follow the tutorial here (
https://ambermd.org/tutorials/advanced/tutorial26/section2.php) as a guideline. I have about 500 ns of trajectory to where I can find a reasonable frame to start my QM/MM/MD.
1.
Do I need to do a restrained QM/MM prior to starting (so after what would be 'equil4.mdin' in this tutorial)? If so, is there a minimum recommendation for how long? I plan on doing dt=0.0005 because of the hydrogen transfer.
2.
Once I start the process, would I put the '&qmmm' into every script for the steered md? Therefore, every round of 25 short MDs would have a QM calculation or am I only doing a small QM/MM/MD restrained equilibration in the beginning followed by Steered MD without QM?
Thanks!
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Received on Wed Oct 02 2024 - 06:30:02 PDT
