AMBER Archive (2004)

Subject: AMBER: Time to minimize the energy by NMODE

From: xiaowei li (xl3a_at_virginia.edu)
Date: Wed Apr 14 2004 - 13:23:02 CDT

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)

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