AMBER Archive (2007)

Subject: AMBER: Fwd: Comparing explicit solvent/vacuum qmmm

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Wed Sep 05 2007 - 06:05:07 CDT

Sorry, a mistake below: dftb was only carried out in vacuum. Anyway, the last
line in mdin below should be deleted for theory=7.
francesco
--- Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> Date: Wed, 5 Sep 2007 00:31:32 -0700 (PDT)
> From: Francesco Pietra <chiendarret_at_yahoo.com>
> Subject: Comparing explicit solvent/vacuum qmmm
> To: Amber <amber_at_scripps.edu>
>
> 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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