[gmx-users] statistics of MD

Anton Feenstra feenstra at chem.vu.nl
Thu May 8 10:35:01 CEST 2003

David van der Spoel wrote:
> On Tue, 2003-05-06 at 08:47, Evka Stefanekova wrote:
>>Dear gmx users,
>>Maybe it's a trivial question, but I would like to know your opinions on 
>>these topics: 

This refers to statistical thermodynamics, which is non-trivial and
often counter-intuitive.

>>Let us have several simulations of the same system prepared. Each of them 
>>has the same parameters, although slightly different initial conditions 
>>(i.e. initial velocities of atoms are slightly different, also some atoms 
>>may be slightly shifted). Let us also assume that the time of run of all 
>>simulations is long enough for the studied phenomenon to finish. Is there 
>>an argument from which we have that these simulations will result into 
>>simillar final states? Isn't it necessary to run several simulations of 
>>the same system and then statistically compute the most probable behavior 
>>of the system? I mean, why we allways run just one simulation of some 
>>system - how is this simulation statistically significant?
> It depends on your system. If you have a simple liquid, all your runs
> will converge to the same values. If you have a single protein in water
> it will most likely not give the same statistics within the same time. 

You should also note the subtleties involved in Evka's statement of "result
into similar final states". This doesn't mean that you will get the same
final structure (ie coordinates), this certainly won't be the case for the
water, and neither will it be for e.g a protein. It means that average
properties will converge (e.g. 'conformational states', clusters, populations,
densities, energies etc.).

Hence, I always try to do as many different simulations of a system that
I can manage, and try to focus on the phenomena that are common in them.


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| 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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