[gmx-users] Criteria and Energy Conservation

gtroiano at if.usp.br gtroiano at if.usp.br
Tue Oct 9 20:45:51 CEST 2007

 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?

 Thanks in advance,

 Gustavo Troiano Feliciano

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