On Wed, Aug 19, 2009, Peter Varnai wrote:
> It is probably a good thread to share an odd experience using NMR
> distance restraints between two molecules and octahedral periodic box
> with iwrap=1.
Thanks for the detailed report. The bottom line from my perspective is:
don't use iwrap=1 if you can possibly avoid it. In particular, don't use
iwrap=1 with NMR-like restraints in place.
> It is probably more complex that this as when a simulation starts from
> molecules in proximity and then iwrap separates them virtually during
> the simulation, it does not seem to affect the restraint energy in the
> actual run, but after restart the behaviour described above will happen.
I think iwrap only affects output coordinates, not the internal ones the
program is using. This would explain the behavior you report.
> It became a bit tricky to run long simulations where I am forced to use
> iwrap but the imaging puts the molecules in a different arrangement back
> to the central box, eg. | A...B | can become | B...A|.
For Amber developers: it seems to me that the "correct" solution here is
to allow binary restarts, so that no one is "forced to use iwrap". Plus, we
could have wrapping code in just one place (ptraj), where there is logic to
have greater control over how wrapping is done that we have in sander/pmemd.
So, is there something broken with binary restarts in the current
code? [The unformatted form doesn't have ltemp0; I don't know what else
might or might not be broken.] If someone could look into this (Scott?)
it would be a great help. This is important enough that we should consider a
patch to Amber10, if needed.
...thanks...dac
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Received on Wed Aug 19 2009 - 23:34:17 PDT
