Hello,
I am working on QM/MM project in which my system is divided into 1) a QM
region of two adjacent amino acids, 2) a mobile MM region that contains all
atoms within 18 Angstroms of one of the QM atoms, and 3) a frozen MM region
consisting of the remainder of the protein and some solvent near the
protein surface. I'm currently equilibrating the mobile MM region for 10 ps
using sander.MPI (from AmberTools 25) while the QM region and outer MM
region are frozen using ibelly=1. The temperature is set to 300 K with
Andersen-type coupling (ntt=2), no pressure coupling. The simulations are
done without PBCs and a nonbonded cutoff larger than my system size. This
is done for 20 replicas that differ only in the geometry of the QM region,
and the initial conformations of the MM regions are identical across
replicas. During this equilibration step, several of the replicas end up
with very distorted and unphysical geometries that cause the simulation to
fail due to SHAKE (used only for hydrogen-containing bonds) giving up. All
of the simulations display negative temperatures throughout the simulation.
The replicas that make it through the 10 ps oscillate around -300 K, while
the ones that fail have their temperatures become very large negative
numbers.
I also tested minimizing the mobile MM region for 5000 steps while keeping
the QM and outer MM regions frozen and slowly heating from 0 K to 300 K,
but this didn't alleviate the geometry or negative temperature problems. I
think that there may be a problem with bad contacts between the mobile MM
and QM regions, but the minimization ought to alleviate that. I'm also very
confused by the negative temperatures. This procedure was used by others in
my group for a similar system in past years, and they didn't run into the
same problems and didn't have any ideas. Does anyone have any advice?
Best,
Matthew Tremblay
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Received on Wed Jul 02 2025 - 08:30:02 PDT
