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
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
____________________________________________________________________________________
Need a vacation? Get great deals
to amazing places on Yahoo! Travel.
http://travel.yahoo.com/
-----------------------------------------------------------------------
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
