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.
>
> 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.
[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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Received on Tue Aug 16 2011 - 05:30:03 PDT
