AMBER Archive (2008)

Subject: Re: AMBER: "radius = 0.000"

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Tue Jul 01 2008 - 11:39:30 CDT

Hi Arturas,

just a wild guess: Is the prmtop or restart file you are using really a
periodic system?

Specifically, take a look at your prmtop file:

%VERSION VERSION_STAMP = V0001.000 DATE = 06/26/08 11:35:29
%FLAG TITLE
%FORMAT(20a4)
pt1
%FLAG POINTERS
%FORMAT(10I8)
     2759 8 2748 11 11 15 24 13 0 0
     3729 915 11 15 13 10 12 4 10 1
        0 0 0 0 0 0 0 XXX 17 0

In the third line, the eigth number, do you have a 1 or 0? A zero would
indicate that it is not setup as a periodic system and that will make
sander fail if you feed it into a ntb=2 simulation. Also check if the last
line of your restart file contains the box dimension and angle.

Post your leap command that built the prmtop if you want, that should make
things clearer...

Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Tue, 1 Jul 2008, Arturas Ziemys wrote:

> Hi,
>
> I have minimized my pretty simple protein+water system. Supplied minimized
> structure (from restart output) to equilibration. My job was hanging forever.
> Using '-o stdout' I saw that my job stalled at after that line is printed:
> "sphere to fit in unit cell has radius = 0.000".
>
> I have tried to find some answer on internet but without success - just one
> similar question. My feeling says that job does not know my systems
> dimensions ? What is the remedy ?
>
> job setup:
> &cntrl
> imin = 0,
> ntx = 1,
> irest = 0,
> ntt = 3,
> gamma_ln = 1.0,
> temp0 = 300.0,
> tempi = 300.0,
> ntp = 1,
> ntb = 2,
> ntf = 2,
> ntc = 2,
> cut = 12,
> dt = 0.001,
> nstlim = 100
> /
>
>
> --
>
> Arturas Ziemys, PhD
> School of Health Information Sciences
> University of Texas Health Science Center at Houston
> 7000 Fannin, Suit 880
> Houston, TX 77030
> Phone: (713) 500-3975
> Fax: (713) 500-3929
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