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
>
>
>
>
>
________________________________________
_______
> AMBER mailing list
> AMBER.ambermd.org
>
http://lists.ambermd.org/mailman/listinf
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)
________________________________________
_______
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinf
o/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Sep 11 2012 - 19:00:04 PDT
