Hi, I want to calculate the normal frequencies of DNA with 5 base pairs.
So I take following steps to get it.
First, using SANDER to minimize the energy, and I got RMS=4.467E-01, and
sandermin.rst.
Second, using NMODE(ntrun=4) to minimize sandermin.rst to get RMS is in
the order of 10^-4.
As David has emailed me before, it just takes a few hours to finish
NMODE minimization ( My computer has two 1.53 GHz AMD Athlon K7 MP
processors with 256KB of cache (per cpu) and 1 GB of RAM).
However, NMODE minimization has run about 50 hrs on my computer and it
is not finished yet. Is there anything wrong with my case? Thank you
for your nice help.
Following is my input and output file for sander mininization:
&cntrl
igb=1, ntb=0, ntpr=50,
cut=999, ntr=0,
imin=1, maxcyc=1000, ncyc=500,
&end
output:
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1000 -3.0607E+03 4.4670E-01 2.5204E+00 N3 372
BOND = 12.5946 ANGLE = 50.9148 DIHED =
229.0234
VDWAALS = -200.7355 EEL = -1637.9778 EGB =
-1382.9776
1-4 VDW = 84.9881 1-4 EEL = -216.5779 RESTRAINT =
0.0000
Following is the input file for the NMODE minimization:
&data
ntrun=4,
nsave=2,
ndiag=2,
cut=10.0,
nprint=1,
drms=0.0001,
maxcyc=500,
scnb=2.0,
scee=2.0,
&end
--
Xiaowei Li
Department of Electrical and Computer Engineering
University of Virginia
924-3446(O)
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 14 2004 - 19:53:00 PDT
