AMBER Archive (2005)

Subject: AMBER: problem with belly calculation restart

From: Ed Pate (pate_at_math.wsu.edu)
Date: Thu Apr 21 2005 - 19:28:59 CDT

I am trying to restart a belly calculation in Amber 7. My input file is

&cntrl
  imin=0,
  irest=1,
  ibelly=1,
  ntx=7,
  ntt=1,
  temp0=300.0,
  ntp=0,
  tautp=0.2,
  ntf=2,
  ntc=2,
  ntb=0,
  dt=0.002,
  nstlim=100,
  ntwe=0,
  ntwx=500,
  ntpr=25,
  ntwr=50,
  iwrap=1,
  lastist=30000000,
  lastrst=30000000,
&end
&ewald
  use_pme=0,
  eedmeth=5,
&end
Belly
RES 9 10
RES 12 14
(rest of belly residues follow)
END
END

The job terminates with the following message in the .out file:

Ewald PARAMETER RANGE CHECKING:
 parameter alpha: (unit cell angle) has value 0.12855-268
 This is outside the legal range
 Lower limit: 0.30000E+02 Upper limit: 0.15000E+03
 Check ew_legal.h

The previous belly calculation (which I am trying to restart) used the
same jobscript as above, except ntx =1 and irest=0. I am using the .rst
file generated in the previous belly calculation. I get the same error
message if I leave out the use_pme=0 and eedmeth=5 statements.

One other observation: In the original simulation that I am trying to
restart, I thought the use_pme=0 and eedmeth=5 statements would turn PME
off. This did not appear to be the case from the output from the original
simulation.

Can anyone help me understand what I am doing wrong?

Thank you for your help.

Ed Pate

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