Hi Francesco,
TSOLVENT and TSOLUTE are from the "good old days" of amber 5. The concept of
a separate calculation of the solute and solvent temperature, or even
actually the concept of solvent and solute, no longer exists in Amber 9.
Thus these two files are just filled with the time step and no data - hence
why you just get a straight line of gradient 1 in xmgr. You can ignore these
two files since for amber 9 runs they have no meaning.
All the best
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Francesco Pietra
> Sent: Wednesday, August 29, 2007 10:41
> To: amber.scripps.edu
> Subject: Re: AMBER: Criteria for classical md being OK to
> move to QM-MM
>
> Hi
> Thanks for meoh spreading out.
>
>
> xmgrace summary.TSOLVENT
>
> gives a straight line, which goes fro 100 to 400 (ordinate
> scale) vs 0 to 2000
> (abscissa). Similar trend for TSOLUTE. Which is confusing me,
> not knowing the
> units 100-400 and 0-2000
>
> francesco
>
>
> --- "M. L. Dodson" <mldodson.houston.rr.com> wrote:
>
> > 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
> > 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.
> > >
> >
> > 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_TSOLVENT
> > > 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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>
>
>
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Received on Sun Sep 02 2007 - 06:07:12 PDT
