On Fri, Mar 31, 2017, Dan Roe wrote:
>
> On Fri, Mar 31, 2017 at 12:30 PM, Chris Neale <candrewn.gmail.com> wrote:
> > If the issue is simply PBC wrapping during the run then that sounds like
> > something that should get fixed in the code at some point, esp given that
> > it's called a "restart" file.
>
> Another alternative is when using positional restraints turn iwrap off
> and use netcdf trajectories and restarts.
If you have positional restraints to a reference structure, you really
should not be using iwrap=1 in dynamics. There is no easy way to be sure
that the reference coordinates and the MD coordinates are being wrapped in
the same way. The internal wrapping in pmemd/sander is not the same as
"autoimage".
Corollary #1: If you don't have positional restraints, you really should not
be using iwrap=1 in dynamics.
Corollary #2: iwrap=1 should almost never be used. Be sure there is no
alternative.
Corollary #3: just don't set iwrap=1. Remove the option from the code and
Reference Manual. Find and correct all web pages and tutorials that recommend
this option. Consider amnesia-inducing drugs that will remove all traces of
this option from your little grey cells.
Corollary #4: don't believe everything you read on the mailing list,
especially in posts like the current one.
....dac
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Received on Fri Mar 31 2017 - 11:30:02 PDT
