AMBER Archive (2007)

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

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Aug 29 2007 - 11:51:15 CDT

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 TEMP PRES
VOLUME DENSITY EPTOT ETOT

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.

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

Thanks

francesco pietra

       
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