AMBER Archive (2008)

Subject: Re: AMBER: "radius = 0.000"

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jul 01 2008 - 11:16:38 CDT

a few things to check first:
have you run all of the test cases?
did they work without error?
is there anything unusual about your system- just standard protein and water?
you might give us some info from leap on how you built it, and
also what kind of simulation gave you the restart file.

On Tue, Jul 1, 2008 at 12:08 PM, Arturas Ziemys
<arturas.ziemys_at_uth.tmc.edu> 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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