On Tue, Aug 16, 2011 at 9:10 AM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Aug 16, 2011, Bruno Rodrigues wrote:
> >
> > I realized that with iwrap=1 the DNA shifts to the border of the box, and
> > sometimes breaks the two strands apart. I reported the problem before at
> the
> > list, but didn't get any clue.
>
> As long as the energies are continuous, this is a visual problem, not any
> real
> problem, and can be corrected in ptraj.
>
Well, sure, but I'm looking at solvation shells, and not having the solue
completely filled with water might be a problem. I also observed a strange
behavior when the DNA comes out of the 1st box. You can see from my last
email an image where the DNA is shifted to border.
>
> >
> > So I decided to switch iwrap off. As the simulation lasts for 40ns with a
> > T-jump from 300 up to 400K, I *guess* the problem is related with
> molecules
> > very far from the solute.
>
> It's not clear what you mean by "T-jump". Does it happen (nearly)
> instantaneously, or do you mean that the temperature slowly rises from 300
> to
> 400?
>
> There is no need to "guess" about problems that might arise without iwrap:
> just search for "*" characters in the restart file. If they are not there,
> you should be fine.
>
> I'm comparing the heating rate, one was heated up from 300K to 400K in 4ns
and the other in 40ns. The restart crashed at 395K and 36ns, just a few
steps from the goal!
There are "***" characters in the restart file. If I generate new restart
files from the last frame of the simulation without velocity, does it change
a lot my dynamics?
> [It would be nice for some developer to really implement and test the new
> netcdf restart format, so that we could (mostly) get rid of the need for
> iwrap
> in sander/pmemd.]
>
> ....dac
>
>
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--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Tue Aug 16 2011 - 13:30:06 PDT
