Although it is true that you may be using a equilibration time that is
too small, and that your heating is too fast, especially since you are
using explicit solvent, the main difficulty in answering your question
is that you also don't mention what properties you are looking at. How
did you conclude that your results after 15ns are "completely
different"? What properties did you measure? How do they differ?
Note that, even with the exactly the same protocol, the precise
trajectories and final structures are expected to differ between two
different simulations.
Cheers,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Mon, Aug 23, 2010 at 6:01 AM, M. Reza Ganjalikhany
<ganjalikhany.gmail.com> wrote:
> Dear all,
>
> I have done two similar MD simulations with a 300 a.a. protein in explicit
> solvent with different equilibration time.
> The first equilibration time was 20ps and the second was 40 ps (from 0 K to
> 300 K) and then I got completely two different results after 15ns MD
> simulations.
>
> Is it normal to obtain such results? How long should be sufficient for such
> system to be equilibrated?
>
> Any help would be greatly appreciated.
>
> Regards,
> M. Reza
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Received on Mon Aug 23 2010 - 07:30:05 PDT
