[EMAIL PROTECTED] 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
[EMAIL PROTECTED] 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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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