[gmx-users] Criteria and Energy Conservation

[gtroiano at if.usp.br]

 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.

 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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