Hello,
I ran into a problem using the SHAKE algorithm and I was curious if anyone had seen anything similar. I have a protein with a ligand attached embedded in a lipid bilayer. I equilibrated this system classically for about 300ns using GPU’s with CUDA from AMBER16 and during that time I used SHAKE.
After about 300ns I then switched to using QM/MM with DFTB2+D and sander MPI. After I switched to using QM/MM with SHAKE, an N-H bond of the peptide backbone of an ILE residue about 15 angstroms from the QM region elongates to 1.33 angstrom when it was 1.01 angstrom for the entire MM equilibration period. If I turn SHAKE off the peptide N-H bond will oscillate around the 1.01 angstrom value. However as soon as I turn SHAKE back on, the bond elongates back to 1.33 angstrom.
Has anyone else seen anything like this?
Best,
Jon
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Received on Sun Dec 27 2020 - 21:30:02 PST
