AMBER Archive (2004)

Subject: AMBER: sander imin=5

Date: Thu Dec 16 2004 - 02:01:45 CST

Hi all,

I am still trying to extract energy values from my MD trajectory file using
sander imin=5 option. My command is like:

$AMBERHOME/exe/sander -O \
                   -i \
                   -o min5_EN.out \
                   -p 1EMB_3_20.prmtop \
                   -c 1EMB_3_20.inpcrd \
                   -r 1EMB_3_20_min_new.rst \
                   -x 1EMB_3_20.mdcrd \
which seems OK and my in file is as follows:

  imin = 5,
  ntx = 1,
  maxcyc = 1,
  dx0 = 0.000001,
  ntb = 1,
  ntr = 0,
  ntt = 1,
  cut = 10,
  ntwx = 1
Sander starts running, but after every step the VDWAALS and ENERGY values
double. After a short time, the VDWAALS values 'burst' and I get unreasonable
energy outputs. I know that these input files are all working, but I cannot get
the same energy results.

Does anybody have a suggestion??

Thanks in advance,
Murat Cetinkaya
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
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