AMBER Archive (2007)

Subject: AMBER: Comparing explicit solvent/vacuum qmmm

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Sep 05 2007 - 02:31:32 CDT

I have carried out qmmm for a couple of conformers made of 98-atoms
non-polymeric single residue. They are in diastereomeric relationship,
isolatable, and NMR data have been collected.

I compared MD in explicit solvents with those in vacuum, starting from
minimized structures by DFT. These, with latest functionals and high basis
sets, are in accordance with NMR data in CDCl3.

MY QUESTION: I tried to make minin and mdin as much as possible comparatively
significant for vacuum vs solvent. I would be very grateful for experts have a
look at my scripts to judge if my runs deserve confidence. From my side I can
add that perl script on mdout/xmgrace revealed (for adequate ps runs) constancy
of summary.TEMP ESCF EPTOT, PRES when solvent, etc, in all cases. Structure
were checked with VMD in all cases.

SOLVENT RUNS:

(1) Initial minimization solvent
&cntrl
imin=1, maxcyc=1000, ncyc=500,
ntb=1, ntr=1, cut=10.0
/
Hold the EQE fixed with strong restraint
500.0
RES 1
END
END

(2) Classical minimization
&cntrl
imin=1, maxcyc=10000, ncyc=4000,
cut=10.0, ntb=1, ntc=1, ntf=1
/

(3)Stage 1 heating of solute/solvent
&cntrl
imin=0, irest=0, ntx=1,
ntb=1, ntr=1, ntc=2, ntf=2,
tempi=0.0, temp0=50.0,
ntt=3, gamma_ln=1.0,
cut=10.0,
nstlim=10000, dt=0.0015,
ntpr=100, ntwx=100, ntwr=1000
/
Keep EQE fixed with weak restraint
10.0
RES 1
END
END

followed by other five stages up to 300K

(4) 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
/

(5)
300K constant temp and pressure qm md
 &cntrl
  imin=0, ntb=2, pres0=1.0, ntp=1,
  cut=10.0, ntc=2, ntf=2,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=1.0,
  nstlim=20000, dt=0.0005,
  ntpr=100, ntwx=100,ifqnt=1
 /
 &qmmm
  qmmask=':1',
  qmcharge=0,
  qmtheory=2,
  qmshake=0,
  qm_ewald=1, qm_pme=1
 /

Similarly for theory 7
____________________________________-

VACUUM RUNS:

(1) Classical minimization in vacuum
&cntrl
imin=1, ncyc=4000, maxcyc=10000,
ntb=0, ntc=1, ntf=1,
cut=25
/

(2)
Stage1 heating from 0K to 50.0K
&cntrl
imin=0, irest=0, ntx=1,
ntb=0, ntt=3,
tempi=0.0, temp0=50.0,
cut=999,
nstlim=10000, dt=0.0005,
ntpr=100, ntwx=100, ntwr=1000
/

Followed by five other stages up to 300K

(3) 300K const temp qm md
&cntrl
imin=0, ntb=0, ntt=3,
tempi=300.0, temp0=300.0,
nstlim=20000, dt=0.0005,
cut=999,
ntpr=100, ntwx=100, ifqnt=1
/
&qmmm
qmmask=':1',
qmcharge=0,
qmtheory=7,
qmshake=0
/

Similarly for theory 2
__________________________

Thanks
francesco pietra

       
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