[gmx-users] Multiple Simulations

[Anton Feenstra]

Mu Yuguang (Dr) wrote:

> Hi,
> 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.

If your initial conditions differ little, and the differences are random,
and also the differences in initial velocity are random, it should be
appropriate to treat the combined trajectories as a single ensemble by
simply taking them together (without any weighting). This ensemble may
still not describe your system at (global) equilibrium, but will
certainly describe correctly it at the state is currently in. So, although
the calculated averages may not tell you what you need or want to know,
they should be statistically (thermodynamically) correct.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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