Yes, that is indeed the problem. Thanks for the bug report!
-Dan
On Tue, Sep 11, 2012 at 7:32 PM, kurisaki
<kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
> Dear Prof. Rou and Dr. Swails, and
> ambers
>
> I resolved the problem; the cause is not
> for NTB=1
> But for the MD-input file.
>
> The wrong one is as it follows:
>
> &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,
> /
>
> The proper one is derived from Amber
> test module,
> I mean the file in
> "~/amber12/test/trajene_box "
>
> &cntrl
> imin = 5, ntx = 1, irest = 0,
> ntt = 1, tautp = 1.0, temp0 = 300.0,
> tempi = 300.0,
> ntc = 2, ntf = 1, ntb = 2,
> ntp = 1, taup = 1.0,
>
> ntwx = 10, ntwe = 0, ntwr = 10, ntpr
> = 10, ioutfm = 0,
> cut = 8.0, iwrap = 1,
>
> The problem is just for "ntpr = 0".
> Setting "ntpr = 0" solves the problem.
>
> Yours sincerely,
>
>
> KURISAKI
>
>
>
>
>
>
> -----Original Message-----
> From: Daniel Roe
> [mailto:daniel.r.roe.gmail.com]
> Sent: Tuesday, September 11, 2012 11:01
> PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] NTB does not work
> for trajectory analysis with IMIN=5
>
> 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
>>
>>
>>
>>
>>
> ________________________________________
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>> AMBER.ambermd.org
>>
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> o/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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> o/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 Wed Sep 12 2012 - 08:00:07 PDT
