[gmx-users] Multiple Simulations

Mu Yuguang (Dr) YGMu at ntu.edu.sg
Tue Jan 13 15:40:01 CET 2004

I also encountered such situations, when I docked a tripeptide onto a
rna molecules. Beginning with nearly same coordinates, but with
different initial velocities, I got four complete different trajectories
lasting 20 ns each. 
Sometimes, we assign them to the heterogeneity of the specific
interaction between two partners. 
But worse case  is that maybe they are just kinetic traps artificially
introduced by the force fields.
It is really hard to average these trajectories.

Dr. Yuguang Mu
Division of Computational and Structrual Biology
School of Biological Sciences
Nanyang Technological University
Singapore 637820
Tel: 0065-67906489
Mail: ygmu at ntu.edu.sg

-----Original Message-----
From: Anton Feenstra [mailto:feenstra at chem.vu.nl] 
Sent: Tuesday, January 13, 2004 7:09 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Multiple Simulations

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

Thanks David B. for the reference!

David vdS. wrote:
> Aha, I somehow (naively) though you meant equilibrium trajectories...
> 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,
> 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/       |
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