AMBER Archive (2008)

Subject: Re: AMBER: "radius = 0.000"

From: Robert Duke (rduke_at_email.unc.edu)
Date: Tue Jul 01 2008 - 11:24:10 CDT

One simple thing to check - is your compiler indeed converting the integer
input value for "cut" to float correctly (should be apparent from the
listing of used values in the mdout file). I actually don't know what the
spec says should happen in a namelist on this, but the intel compiler will
do the correct conversion for you; most folks I believe would bother to
specify 12.0 in the mdin for cut. This may not be it at all; other worries
would be if the input prmtop/inpcrd from leap are actually what you think
they are (for a solvated system).
Regards - Bob Duke
----- Original Message -----
From: "Arturas Ziemys" <arturas.ziemys_at_uth.tmc.edu>
To: <amber_at_scripps.edu>
Sent: Tuesday, July 01, 2008 12:08 PM
Subject: AMBER: "radius = 0.000"

> 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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