Hello all,
I am seeing very strange behavior equilibrating a QMMM system prior to steered MD runs. 3 hydrogens from the guanidinium group of an ARG spatially adjacent to, but not part of, the quantum region dissociate (i.e., the ARG is part of the classical region). There is a single water in the quantum region (QR), and the QR contains components from a modified DNA sugar and two residues of the enzyme protein, as well. The run is done with iwrap=1 and ntc=ntf=2, but qmshake=0, since the production SMD run to follow will involve proton transfers (dt=0.0005 to compensate). The equilibration uses ncsu_smd with a sum of two distances collective variable held constant at its starting value. As expected, the CV is observed to not significantly change over the course of 1ns of simulation (2000000 steps). The distances comprising the collective variable are between atoms in the QR. The system is being run with sander.MPI modified to incorporate the LCOD ncsu collective variable (I have extensive experience with this modification and have seen no other problems with it). 8 processors are used in the simulations. The input file and qmmm_region.pdb files are attached.
Does any one have any suggestions what might cause this (amazingly strange) behavior?
Thanks,
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Thu Feb 11 2010 - 13:00:02 PST
