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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Jul 02 2008 - 06:07:42 PDT
