[gmx-users] Criteria and Energy Conservation

David van der Spoel spoel at xray.bmc.uu.se
Wed Oct 10 14:13:00 CEST 2007

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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