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 min5_EN.in \
-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:
minimization_step1
&cntrl
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
Murat CETINKAYA
Biomolecular Materials Lab,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176
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Received on Thu Dec 16 2004 - 08:53:00 PST
