Re: AMBER: Criteria for classical md being OK to move to QM-MM

From: M. L. Dodson <>
Date: Wed, 29 Aug 2007 12:11:29 -0500

Francesco Pietra wrote:
> For a 98-atoms non polymeric molecule in meoh
> solvatebox EQE MEOHBOX 15
> I have carried out, in sequence:
> (1) minimization of solvent alone.
> (2) minimization whole system.
> (3) Heating in six steps from 0K to 300K.
> (4) Pressure equilibration according to:
> Equilibrate pressure and 30ps md
> &cntrl
> imin=0, irest=1, ntx=7,
> ntb=2, pres0=1.0, ntp=1,
> taup=2.0, cut=10.0, ntr=0,
> ntc=2, ntf=2,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=1.0,
> nstlim=20000, dt=0.0015,
> ntpr=100, ntwx=100, ntwr=3000
> /
> After 150ps of the latter, I observe (perl script & xmgrace) constant
> Though, the solvent box (parallelepiped intended for later QM-MM) is
no more as
> neat as I expected: some meoh molecules are somewhat outside. Is that
a warning
> that the system is not yet ready for QM-MM? If so, what next to do?
The solute
> is OK.

This is expected and is caused by the solvent molecules diffusing
out of the primary box of the periodic boundary conditions
treatment. See the discussion of the iwrap variable on pages 91
and 92 of the manual. Essentially, you can treat this two ways,
(1) set iwrap=1 which will mess up solvent diffusion calculations,
but is probably the best course if you are going toward QMMM. Or
(2) image the solvent back into the primary box with ptraj during
the analysis phase (see MANY postings on this list for guidance).
Post processing will be a problem if you use the trajectory file
to generate the starting structure for QMMM as trajectory files
have no velocities. Restart files have the velocities. Iwrap=1
is easier for your purpose, I believe. A single step of dynamics
with iwrap=1 should do the trick.

> Are somewhere guidelines how to interpret xmgrace plots for
> summary_TSOLUTE?

Both should be stable, i.e., a straight, flat line, I would suppose.

Bud Dodson

> Thanks
> francesco pietra

M. L. Dodson
Email:	mldodson-at-houston-dot-rr-dot-com
Phone:	eight_three_two-56_three-386_one
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Received on Sun Sep 02 2007 - 06:07:11 PDT
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