On Fri, Sep 25, 2015 at 1:17 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> what do you mean by the results not being the same? the initial MD differ,
> or the overall results (populations etc)?
> using different compiler or CPU (or # threads for MPI) can cause divergence
> in the MD run fairly quickly. results must be well converged to be reliable
> across different machines (or even across runs on the same machine with
> different random seeds).
>
Thanks for the reply.
The overall results differ.
Actually I was testing a small 1ns simulation with 1000 exchanges (each
1ps) expecting exactly the same results (energy/rmsd/exchanges), but it not
seems to be the case.
The fact is that I'm really going to need my simulations to be small as 1ns
(they are part of a protocol that I intent to use for helping PSP). At
least on the beginning of the protocol, I'm more interested on sampling
than convergence.
The initial MD results do not differ... but over time I got different
sampling.
Could I use the same # of MPI threads to have the same sampling (desktop vs
cluster)?
Looking at .mdouts I found that MD values are quite similar (at the
beginning) and that's why I thought the MC metropolis calculation was the
problem.
Could I monitor the exchange ratios, average energies, # of tunneling
events and canonical probability distribution of energy to have sure that
my results are reproducible with an acceptable deviation?
--
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
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Received on Fri Sep 25 2015 - 10:00:03 PDT
