Thanks Dan,
Will changing the trajectory format mid-simulation matter for creating a T
trajectory from all the remd simulations?
-David
On Tue, May 7, 2013 at 1:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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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> >>
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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 - 11:30:05 PDT
