AMBER Archive (2009)

Subject: RE: [AMBER] Particle-mesh Ewald method

From: Ross Walker (
Date: Mon Mar 09 2009 - 14:53:52 CDT

Hi Yunjie,

> Using Amber 9, I am trying to do molecular simulations in TIP3P explicit
> solvent models. The RNA molecule has 12 nt, 11 Na+ were randomly placed. I
> want to use particle-mesh Ewald method with a cutoff of 9 angstrom to
> distinguish short-range and long-range interactions. This would be too big
> for QM system, I do not want to use QM system. Can anyone tell me how to
> write the input file?
> My input file:
> &cntrl
> > imin=0, nstlim=10000000,
> > dt=0.002,
> > ntt=1, tempi=0.1, temp0=300.0,
> > ntb=1,
> > ntf=2, ntc=2,
> > cut=9.0,
> > ifqnt=1

Set ifqnt=0 to turn off QMMM or just remove it from the namelist. PME is
used by default when you run periodic boundaries in Sander/PMEMD so there is
no need to explicitly turn it on. There is nothing special about PME
requiring QMMM to work, I think you may be confused here with work that
sought to make PME work with QMMM in addition to straight MM which it has
worked with since AMBER 6.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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