Hi,
"Wrapping" just means shifting a molecule to the opposite side of the
periodic box when it drifts outside the box boundaries. This prevents
molecules from drifting too far and creating coordinate overflows
(this is more of a problem with ASCII trajectories and restarts, not
as much with NetCDF). This can prevent direct calculation of things
like diffusion; however, cpptraj/ptraj both have the 'unwrap' command
which can be used to remove the effects of imaging based on a
reference frame prior to processing a coordinate frame.
If you are worried about coordinate overflows I recommend using NetCDF
trajectories and restarts (ioutfm=1 and ntxo=2 respectively).
-Dan
On Tue, May 7, 2013 at 10:17 AM, David Winogradoff <dwino218.gmail.com> wrote:
> After examining my restart files and carefully checking the Amber 12
> manual, I concluded that it is several lines in specific restart files that
> are the problem and that turning "iwrap" on could potentially solve the
> problem. The Amber 12 manual says that turning this tag on doesn't
> influence the forces and velocities, but I am concerned it could influence
> my analysis, especially since I will be turning on the tag mid-simulation.
> Could someone provide a comprehensive explanation of "iwrap"?
>
> Thanks,
> David
>
>
> On Mon, May 6, 2013 at 3:49 PM, David A Case <case.biomaps.rutgers.edu>wrote:
>
>> On Mon, May 06, 2013, David Winogradoff wrote:
>>
>> > ... due to Open MPI failures.
>>
>> OK: *my* favorite answer: build your own MPI installation, by using the
>> configure_openmpi or configure_mpich scripts in AMBERHOME/AmberTools/src.
>> That way, you know you are getting the right compiler, nothing outside the
>> Amber tree is referenced (so you don't need to worry about what MPI
>> installations might or might not be on your computer), etc. Also, this
>> more
>> or less automatically gets you an up to date version.
>>
>> Also, if you build MPI using our scripts, we have a reasonable shot at
>> debugging errors. If you are using something from
>> "/cell_root/software/openmpi/1.4.3/gnu/sys/lib" (your example), we have
>> only
>> very indirect knowledge to go on.
>>
>> ...dac
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Tue May 07 2013 - 11:00:02 PDT
