AMBER Archive (2007)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Oct 29 2007 - 15:06:45 CST

Hi Seth,

I would not use Amber 8 to run QMMM simulations there are numerous problems
with it that it has not been possible to fix. You should upgrade to Amber 9
which has a completely new QMMM implementation.

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Seth Lilavivat
> Sent: Monday, October 29, 2007 13:40
> To: amber_at_scripps.edu
> Subject: AMBER: AMBER 8: QMMM - molecule fluctuates wildly
>
> 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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