[gmx-users] Multiple Simulations

Anton Feenstra feenstra at chem.vu.nl
Tue Jan 13 12:07:01 CET 2004

David L. Bostick wrote:
 > Yes, there is a way to combine statistics from various simulations of the
 > same system. [...]

Thanks David B. for the reference!

David vdS. wrote:
> Aha, I somehow (naively) though you meant equilibrium trajectories... My
> experience is that the bad structures have higher energy, not rigorous
> though. Have you seen the recent paper from the Alan Mark group on
> comparison of NMR and Xray structures, all simulated for a long time?
> Not surprisingly, the Xray structures are more stable (so indeed, forget
> about homology models, even though I have just published a paper on
> simulations of those... [J. Comp. Aid. Mol. Des. 17, p 551 (2003)]).

Yes, I even spoke to Fan Hao about his method on a national conference
in the Netherlands (you know which...), it is a nice result although a
little harsh on the NMR people ;-{ I must say, though, that I have found
quite reasonable results with a homology model of my own, that shows
'x-ray' level rms deviations in several 10 ns free simulations. So, all
is not lost. I also saw your paper by the way, which is encouraging for
all of us working on homology models...

But back to combining multiple simulations, I actually want to apply it
to substrate binding studies, where I take several docked orientation
of the substrate in the active site as starting conformations. There,
as with X-ray vs. homology model, it is not a priori known what the
relative weights of the docked orientations (and the corresponding MD
generated ensembles) should be. I had expected before I started the work
that I would get sufficient overlap between trajectories to weigh them,
but that hasn't happened; my substrates are simply too sticky and often
stay in a certain bound state for more than a nanosecond. In other
words, I do not see convergence between trajectories and little if any
signs that convergence will improve fast enough to reach it in the

P.S., have you ever seen a protein simulation in equilibrium...? ;-)


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
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