Dear Ross,
Thank-you very much for your detailed reply, it was very helpful. Just
another quick(!) question (which is more about general MD than AMBER
itself):
> One key thing to remember
> is that MD simulations will only conserve energy for equilibrated systems
> which yours was not, the density was way too low so this may well have
> contributed to the problems you see.
I was under the impression that, as long as the system doesn't have any
'hot-spots' (overlapping atoms/massive forces) and the timestep is
chosen reasonably well (small enough to sample the quickest oscillations
well but not so small that large roundoff errors begin to creep in) then
an NVE simulation should approximately conserve the system's total
energy, i.e. there will be fluctuations but no long-term drift (since
the numerical approximation is the exact solution to a 'nearby' Hamiltonian)
I ran a pure MM simulation on the input files I sent before, using SHAKE
and a large 2fs time step, which from what other have said is on the
verge of instability, and there seemed to be no long term energy drift.
This seems to suggest that my system was equilibrated enough not to
cause major problems.
Or am I missing something? If not, then should a system be 'even more
equilibrated' for a QM/MM run, i.e. are QM/MM runs more sensitive than
pure MM to non-equilibrated conditions?
Thanks again,
Steve.
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Received on Sun Jan 27 2008 - 06:07:04 PST
