[gmx-users] Criteria and Energy Conservation

[gtroiano at if.usp.br]

 Well, yeah. But I want to look at the HOMO-LUMO gap of the system in the living
environment. Since the system is too big to do MD with the QM code, I tried to
use the best force field description I could, and the smallest box as well, to
get structures that could represent the system at 300K. And the forces from QM
are not so bad so far, within the order I'd expect from MD with the QM code.
Anyway, thanks very much for the hints so far, David, and if you have some
suggestion or anything at all to add, feel free to do so.

> gtroiano at if.usp.br wrote:
> >  Thank you very much again, David! Then it's fine for me, since what I want
> to
> > do is a single point QM in "termalized" snapshots of the dynamics and not
> QM
> > minimization.
> But then you will get systematically incorrect energies due to weird
> (force field dependent) bond lengths etc.
> >
> >  Gustavo
> >
> >> gtroiano at if.usp.br wrote:
> >>>  Dear GROMACS Users,
> >>>
> >>>  I'm trying to use GROMACS to get some MD snapshots for single-point
> >> quantum
> >>> mechanical calculations, trying to observe HOMO-LUMO gap of a protein
> >> immersed
> >>> in water with counterions, at a given salt concentration (4600 atoms in
> >> total).
> >>> I'd like to know if they are reliable enough to send to QM calculations.
> >> I've
> >>> got two questions: Which are the criteria I should be looking at? And one
> >> of
> >>> them I've analyzed was energy conservation (I'm doing 300K NVT MD, with
> 10A
> >>> cutoff for vdw and coulomb, with PME electrostatics, and double
> precision),
> >> and
> >>> the manual says a Ekin RMSD/Tot Energy RMSD ratio below 0.05 is fine, but
> >> I've
> >>> got 0.3-0.5 in all simulations I've done. What should I do?
> >>>
> >> This is because of T coupling. If you turn off T coupling it will be
> >> better (but you will not have constant T, and the energy will dirft in
> >> the long run). Your starting structures are fine for QM, but QM
> >> minimization will take a LONG time.
> >>
> >>
> >>>  Thanks in advance,
> >>>
> >>>  Gustavo Troiano Feliciano
> >>>
> >>>
> >>> ----------------------------------------------------------------
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> >>
> >> --
> >> David van der Spoel, Ph.D.
> >> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> >> Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
> >> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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> >
> >
> >
> >
> > ----------------------------------------------------------------
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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