Yes. You should set a new ig value on each restart to prevent
synchronization.
On Fri, Sep 3, 2010 at 1:19 PM, colvin <colvin4367.gmail.com> wrote:
> Dear all,
>
> When i was reading the manual for temperature regulation, i saw a
> statement: "Since Langevin simulations are potentially susceptible to
> "synchronization" artifacts, you should explicitly set the ig variable
> (described below) to a different value at each restart of a given
> simulation."
>
> I check amber mailing list for this ig value as well...and in one of
> the tutorial (Loop Dynamics of the HIV-1 Integrase Core Domain) ig
> value was used.
>
> If i want to use ntt=3 and run the 1.8 ns of simulation by 9x200ps
> run, as shown by amber workshop tutorial-A Practical Example (A-DNA),
> do i need to set ig value? Because the tutorial does not set this ig
> value.
>
> in short, all simulations that use ntt=3, regardless the system size
> and nature, will need to set ig value? same for sander and pmemd?
>
> Thanks and regards,
>
> Colvin
>
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Received on Fri Sep 03 2010 - 01:30:03 PDT
