Hi,
Thanks David, it helps when you know there is light at the end of the
tunnel.
Using PME didn't have any effect, but using a full precision trajectory
reproduced energies up to 5e-3 kJ/mol. So the imprecision of the xtc
coordinates causes the inaccuracy of the energies, i.e. creates a
systematic bias towards high energies. This can actually be explained by
the fact that bonded potential energy functions have a positive second
derivative, as well as the Lennard Jones potential in the region which
contributes most to the total energy. It is easy to see that a random
and symmetric noise epsilon on the position x (truncation error in the
xtc file) gives values of U(x+epsilon) whose average is larger than U(x)
if U''(x) > 0.
As far as I am concerned, I don't have the trr files anymore for my
system. I can forget about accurate energies... But it's good to know
that the effect exists, and can lead to biases of the order 2.5% on
bonded energies with the xtc precision.
Bye,
Michel
So I guess what I'm saying is that in principle you should be able to
get good energies with rerun. Maybe you should try and narrow down the
problem by doing some testing:
(a) Do some reprocessing with PME rather than RF to see if that helps.
(b) Do some reprocessing on full precision trajectories rather than
xtcs to rule out precision issues
etc.
Best wishes,
David
==========================================================
Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
==========================================================
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