AMBER Archive (2008)

Subject: AMBER: "radius = 0.000"

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Tue Jul 01 2008 - 11:08:45 CDT

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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