Hi,
As long as the trajectories have temperature information there should
be no problem mixing formats.
-Dan
On Tue, May 7, 2013 at 12:27 PM, David Winogradoff <dwino218.gmail.com> wrote:
> 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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>> AMBER mailing list
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 - 14:00:02 PDT
