On Tue, Nov 24, 2015 at 9:56 PM, Charles Lin <clin92.ucsd.edu> wrote:
> I believe the manual refers to any post processing you may want to make
> with your system. I'm not 100% certain about this, I would have to go
> check the code, but assuming you're running diffusion using COM
> restraints. You may be getting the wrong distance in DUMPAVE if you turn
> iwrap=1 because when your molecule moves to the top of the box it comes
> back in the bottom so you'll not get a true distance but essentially the
> wrapped distance if you were using center of mass restraints.
>
> If you're doing anything that requires your "real" coordinates and need to
> post process things it may be better to run iwrap=0 and then post process
> using cpptraj.
>
​Good advice. The only addition I'll make is that if you use iwrap=0, you
should *also* use ntxo=2 and ioutfm=1 to write coordinate files to NetCDF
format (this avoids overflowing the ASCII formats and ending up with
useless coordinate or trajectory files).
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 24 2015 - 21:00:04 PST
