AMBER Archive (2007)

Subject: AMBER: AMBER 8: QMMM - molecule fluctuates wildly

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Mon Oct 29 2007 - 14:40:06 CST

Dear Amber Users,

I am running a QMMM MD simulation. The system is 28 atoms large (not
including waters). When I view the trajectory, the molecule begins to
oscillate wildly and becomes very distrorted by the end of a 1000fs
run. I reduced my time step to 0.5 fs but still have the same
problem. Do I need to put some restraints on my solute? If so, what
is the syntax for applying a restraint on a set of atoms with the
ntr=1 option in a QMMM.in file.

Thanks,
Seth
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