On Thu, Apr 30, 2015 at 1:55 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> Sorry if I am jumping in on someone else's conversation...
>
> I remember hearing something about "errors in the forcefield building up
> over long timescales"
>
> It was something about restarting jobs every ~100 ns to make sure that
> didn't happen.
>
> That being said, I can't seem to find that question nor the citation. I
> thought it was my Mertz or Simmerling, but google isn't helping.
>
> Am I just dreaming this or can one of the experts chime in?
>
I've said similar things in the past (I'll call it "informed
speculation"), but primarily in reference to running 20 1ns simulations
rather than 1 20ns simulation. But this is a bit different from the
discussion at hand -- what you're referring to involves running 20 ns
simulations with different random seeds starting from the same structure
(or something like that). The conversation here is talking about running a
single long simulation by breaking it into chunks and restarting short
simulations from the final snapshot of the previous one.
I'm not sure exactly what/whose comment you're remembering, though.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Apr 30 2015 - 11:30:02 PDT
