Unfortunately trajectory post-processing is not very comfortable with
a changing box size, so any hacking to get it to work can lead to
unexpected results. What version of Amber are you using? Does your
installation pass all test cases? If so I think this issue may be
difficult to debug remotely. If you would like to send me (off-list)
the topology, input coords, and at least 2 frames of the trajectory I
could take a look at this for you.
-Dan
On Tue, Sep 11, 2012 at 7:08 AM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Thank you for your reply, Jason.
>
> The error "TRAJENE WARNING: nfft size
> would change with this box!"
> Is resolved by setting the box size of
> inpcrd to that of mdtraj.
>
> However, calculation does not work yet.
> Simulation was quit by following
> messages,
>
> POST-PROCESSING OF TRAJECTORY ENERGIES
> TRAJENE: Original NFFTs: 60 60
> 60
> trajectory generated by ptraj
> |Largest sphere to fit in unit cell has
> radius = 28.881
> minimizing coord set # 1
> (END)
>
>
> Following message appears on the
> display.
>
> forrtl: severe (71): integer divide by
> zero
> Image PC
> Routine Line Source
>
> sander 00000000004B26DB
> Unknown Unknown Unknown
> sander 00000000004A32D2
> Unknown Unknown Unknown
> sander 00000000004A0BC2
> Unknown Unknown Unknown
> sander 000000000049B27B
> Unknown Unknown Unknown
> sander 00000000004094C2
> Unknown Unknown Unknown
> libc.so.6 0000003D5081EC5D
> Unknown Unknown Unknown
> sander 00000000004093E9
> Unknown Unknown Unknown
>
>
> I guess there is any other problem in
> the input files...
>
> Sander was executed by the following
> MD-input file:
>
> &cntrl
> imin = 5, igb = 0,
> ntx = 1, maxcyc = 1,
> ntc = 2, ntf = 2,
> ntb = 1, ntp = 0,
> ntwe = 0, ntpr = 0, ntwx=1,
> cut = 9, idecomp = 0,
> /
>
>
> Yours sincerely,
>
>
> Kurisaki
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 Sep 11 2012 - 07:30:10 PDT
