RE: AMBER: QM/MM NPT Simulation

From: Ross Walker <>
Date: Fri, 20 Apr 2007 08:22:25 -0700

Dear Daniel,

> 300K constant temp QMMMMD - 250ps Equilibration
> &cntrl
> imin=0, irest = 1, ntx = 5,
> ntb=2, pres0 = 1.0,
> ntp=1, taup=2.0,
> ntc=2, ntf=2, cut=6.0,
This is far too small - the absolute minimum is 8.0! I recommend setting
this to 8.0 and qmcut (in the qmmm namelist) to 10.0 or 12.0. If you get
messages about the cutoff being too big then you need to add more solvent
around your system.

The issue here is that the cutoff for QM calculations is essentially a
surface at cut distance from the QM region rather than a pair-pair cutoff.
Thus any atom that is within cut of any QM atom is included in the
interaction list for ALL QM atoms. There are theoretical reasons for this
related to SCF convergence but what it entails is that the cutoff off
boundary for QM calculations is larger than for the MM part. In periodic
systems what this entails is that since the direct space calculation mustn't
see it's own image so for pure MM systems the smallest box dimension must be
longer than the cutoff. For QM/MM calculations the smallest box dimension
must be larger than the qmcut (=cut by default) + the size of the QM region.

So, try setting cut=8.0 (and qmcut=10.0) and running again. If you see a
bomb because the box size is too big then go back to the setup and make your
methanol box bigger.

> I have continued the PMEMD simulation into the production phase so I
> dont think the problem has to do with the drug-methanol system. I have
> also tested the QM/MM equilibration with ntt=3 but got the same
> problems.

Did you use cut=6.0 for the classical calculation?

If you still have problems after using a bigger cutoff please send me the
files you used to create the prmtop and inpcrd files along with the leap
commands you used and I'll try it out myself.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Apr 22 2007 - 06:07:44 PDT
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