AMBER Archive (2007)

Subject: AMBER: Too big EEL energy in energy minimization

From: Wang, Xuelin (Xuelin.Wang_at_stjude.org)
Date: Thu Sep 13 2007 - 09:34:27 CDT


Dear Amber users:

I got a problem when I did an energy minimization using sander with
igb=2. after 200 steps, 1-4 EEL energy is too big (see below output). I
checked the pdb file at the 200 step, it seems that hydrogen atom is too
close to nearby opposite charged atoms. I looked through Amber Archive.
someone have the similar problem as mine. it is probably caused by
"coulomb singularity". but I didn't find any way to fix it. Could Anyone
who know the answer please let me know?

Thanks
Xuelin

input for minimization:

 &cntrl
  imin = 1,
  maxcyc= 200,
  ncyc = 200,
  ntb = 0,
  igb = 2,
  cut = 10
 /

output until 200 step

   NSTEP ENERGY RMS GMAX NAME
NUMBER
      1 2.2320E+14 5.5226E+13 6.1959E+15 C212 15050

 BOND = 7614.5838 ANGLE = 10295.7603 DIHED =
7006.8784
 VDWAALS = ************* EEL = -17172.9293 EGB =
-5767.1696
 1-4 VDW = 2826.7528 1-4 EEL = -6029.6140 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME
NUMBER
     50 7.5926E+04 1.1788E+02 1.5699E+04 C311 11126

 BOND = 43183.3868 ANGLE = 16384.4780 DIHED =
7211.9227
 VDWAALS = 34584.4697 EEL = -16844.8052 EGB =
-6150.0674
 1-4 VDW = 3575.6091 1-4 EEL = -6019.1613 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME
NUMBER
    100 -8.6078E+03 6.5207E+00 4.3093E+02 C313 1532

 BOND = 3016.2527 ANGLE = 8808.6151 DIHED =
6951.3959
 VDWAALS = -999.9839 EEL = -16880.7853 EGB =
-6252.7447
 1-4 VDW = 3056.8384 1-4 EEL = -6307.3457 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME
NUMBER
    150 -2.6681E+06 3.9955E+08 6.2474E+10 H2 4038

 BOND = 2362.1843 ANGLE = 7920.8575 DIHED =
6911.7297
 VDWAALS = -1862.9807 EEL = -16849.7311 EGB =
-6275.6945
 1-4 VDW = 2949.4612 1-4 EEL = -2663244.3069 RESTRAINT =
0.0000

   NSTEP ENERGY RMS GMAX NAME
NUMBER
    200 -5.7480E+07 1.8690E+11 2.9224E+13 H2 4038

 BOND = 2362.1857 ANGLE = 7920.8598 DIHED =
6911.7297
 VDWAALS = -1862.9802 EEL = -16849.7310 EGB =
-6275.6947
 1-4 VDW = 2949.4612 1-4 EEL = ************* RESTRAINT =
0.0000
  MAXIMUM NUMBER OF F EVALUATION EXCEEDED

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