it's important to note that the tutorials are meant as general examples of
how to perform a particular simulation. However, one should not expect that
the input files are always exactly correct for the work you need to do.
Sometimes the runs are too short for real production work, and sometimes
methods and options are updated in the literature but tutorials are not
rewritten, and sometimes your system just needs different treatment. It's up
to the user to keep up with the literature on simulations and adjust their
real production work accordingly. The tutorials are general guides, not
input files to be copied exactly. Of course it's definitely ok to ask
questions if you're unsure- I just wanted to clarify this information about
the tutorials because this kind of question comes up frequently.
>
> > 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
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Sep 03 2010 - 05:30:04 PDT
