Im going to extend the simulations until convergence in order to get
reproducible and more reliable results. Thank you Carlos, Jason and Gustavo
for the comments.
Em 25/09/2015 15:18, "Gustavo Seabra" <gustavo.seabra.gmail.com> escreveu:
> Hi Thiago,
>
> Just to add my R$0,08 to what the others have already said here…
>
> Remember that MD is a chaotic system. With 14 replicas, you have 14
> chaotic systems exchanging information using random number-based MC
> exchanges to connect them. The fixed ig you use is just the seed for the
> random number generator, but there are many different factors that can
> influence the exact trajectory that each replica will follow.
>
> In the end, as pointed out, what you can compare between MD runs are the
> final overall results, such as thermodynamic averages, populations, etc.,
> and even this is assuming all your calculations are properly converged
> before you can gather the data.
>
> So, in the end, yes, you should be expecting differences for your systems.
> Different runs, even on the same machine (unless using sander or
> pmemd.cuda, as Jason pointed out) will sample different regions of the
> phase space over time. If the calculations are converged you are assuming
> all regions have been properly sampled, but there’s no control over the
> order of the sampling. In a short amount of time, the regions sampled over
> the same time may be different for each calculation, and the calculations
> may be far from converged.
>
> Gustavo Seabra
>
>
>
> > Em 25/09/2015, à(s) 13:11, Thiago Lipinski Paes <thiagopaes.gmail.com>
> escreveu:
> >
> > Dear Amberists,
> > I'm trying to analyze the behavior of a T-REMD simulation both on Cluster
> > and Desktop, using MPI.
> > I'm using the same .mdins (with a fixed ig=77777) to see if I can
> reproduce
> > my Desktop results, but faster.
> > I'm using 14 replicas (ng=14), with ng=70 (Cluster) and ng=28 (Desktop).
> > The results are not the same.
> > Can I say this is an effect of MC-Exchanges? Should I be expecting this
> > kind of difference?
> >
> > Thanks in advance.
> >
> > thiago
> >
> > --
> >
> > Thiago Lipinski Paes
> > Computer Engineer - Computer Science MSc - Computer Science PhD Candidate
> > Laboratório de Bioinformática, Modelagem e Simulação de Biossistemas
> (LABIO)
> > Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS)
> > Av. Ipiranga, 6681 - Partenon - Porto Alegre/RS - CEP: 90619-900
> > Tel: +55 51 33203611 ext.8602
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Sep 25 2015 - 12:30:03 PDT
