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

From: Francesco Pietra <chiendarret.yahoo.com>
Date: Wed, 29 Aug 2007 09:51:15 -0700 (PDT)

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


       
____________________________________________________________________________________
Got a little couch potato?
Check out fun summer activities for kids.
http://search.yahoo.com/search?fr=oni_on_mail&p=summer+activities+for+kids&cs=bz
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Sep 02 2007 - 06:07:11 PDT
Custom Search