Dear Amber community,
A feature I found in my simulation these few days was that when I applied Cartesian restraints (ntr=1) to part of my protein (e.g. terminal residues or Zinc finger so that the zinc ion doesn’t fly out), the flexibility of this protein itself, and also movement of another bound protein, apparently increases. When I change the restraints into internal distance restraints (nmropt=1) for the same region, such increased conformation search speed is gone. Things slow down apparently.
Why is this happening, my rough guess is that this maybe has to do with the Langevin thermostat; when using absolute restraints, the random forces from the thermostat is not dissipated into translational and rotational motion, therefore it turns into internal energy to make the protein flex around much more.
I set gamma_ln=0.01 in opc water.
Is this phenomenon commonly seen, or somewhat seen, by others also? And if so, was the reason what I had speculated? Very curious.
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Received on Tue May 18 2021 - 21:00:02 PDT
