On Tue, Mar 8, 2016 at 6:05 PM, Timothy Christopher Schutt
<tschutt.mymail.mines.edu> wrote:
>
> .Daniel: I'm having trouble compiling the beta cpptraj - I'm pretty new to
> linux and command line stuff so I'm sure that part is just me being slow
> but I'll figure it out here eventually.
If you give some more specifics about what is going wrong I may be
able to help. With the latest GitHub version of cpptraj with Amber
already installed and AMBERHOME correctly set it should be as simple
as:
./configure -amberlib gnu
(Assuming of course you are using gnu compilers). Let me know if you
need any more help,
-Dan
>
> .Thomas: I just attempted the unwrap command and that totally worked!!
> Thanks! I'll be sure to include that from now on. I didn't realize that was
> required at first because the diffusion command automatically accounted for
> wrapping around in one dimension at a time.
>
> On Tue, Mar 8, 2016 at 5:34 PM, David A Case <david.case.rutgers.edu> wrote:
>
>> On Tue, Mar 08, 2016, Timothy Christopher Schutt wrote:
>> >
>> > ...one molecule sitting on the box edge or corner happens to cross the
>> > boundary in two different dimensions during the same frame change. In
>> > this scenario the wrapping of the second periodic boundary is not
>> > accounted for and the MSD jumps up by n * L^2/N (L= simulation box
>> > length. n= number of molecules in the mask double wrapping that frame,
>> > and N = the number of molecules in the mask).
>>
>> Are you trying to compute diffusion behavior from a trajectory that was
>> originally created with iwrap=1? Or that has been subject to the "image"
>> or
>> "autoimage" command in cpptraj? Just trying to pin down possible sources
>> of
>> problems.
>>
>> ....dac
>>
>>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Mar 08 2016 - 21:00:03 PST
