AMBER Archive (2002)

Subject: BLOWUP after 100 ns???

From: Randy M. Wadkins (rwadkins_at_flash.net)
Date: Thu Sep 19 2002 - 15:51:28 CDT


Under the general heading of "What the...??" After over 50000 MD
steps, I get the following, using the following parameters in sander,
from Amber 7:

   run MD at 300K
  &cntrl
         imin=0,
         ntc=2, ntf=2,
         cut=12.0, igb=1, saltcon=0.2, gbsa=1,
         ntpr=50, ntwx=50, ntwe=50,
         nstlim=500000, dt=0.002,
         ntt=1, tempi=300.0, temp0=300.0, tautp=2.0,
         ntx=5, irest=1, ntb=0, ntwr=500,
         nscm=500,
  &end

Note that this is using the generalized born solvation, no periodic
box, and no explicit solvent, no constant pressure. It's also a 1
residue mutant of a protein that the simulation completed without a
hitch.

Last 3 entries in the the mdout file:

  ------------------------------------------------------------------------------

  NSTEP = 49950 TIME(PS) = 109.900 TEMP(K) = 302.28 PRESS = 0.0
  Etot = -6456.5702 EKtot = 5654.5567 EPtot = -12111.1269
  BOND = 1481.1060 ANGLE = 3924.9687 DIHED = 2864.6773
  1-4 NB = 1677.2196 1-4 EEL = 23320.8047 VDWAALS = -4004.8780
  EELEC = -34835.6569 EGB = -6636.2259 RESTRAINT = 0.0000
  ESURF = 96.8575
  ------------------------------------------------------------------------------

    KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

    Translational and rotational motion removed

    KE Trans = 0.0000 KE Rot = 0.0000 C.O.M. Vel = 0.000000

  NSTEP = 50000 TIME(PS) = 110.000 TEMP(K) = 300.37 PRESS = 0.0
  Etot = -6459.8592 EKtot = 5618.8823 EPtot = -12078.7415
  BOND = 1494.4896 ANGLE = 3984.1520 DIHED = 2879.9049
  1-4 NB = 1656.9092 1-4 EEL = 23260.8580 VDWAALS = -3995.7676
  EELEC = -35160.8665 EGB = -6295.2657 RESTRAINT = 0.0000
  ESURF = 96.8446
  ------------------------------------------------------------------------------

  NSTEP = 50050 TIME(PS) = 110.100 TEMP(K) = 544.48 PRESS = 0.0
  Etot = 6487.8520 EKtot = 10185.3119 EPtot = -3697.4600
  BOND = 4893.8028 ANGLE = 4553.4939 DIHED = 2939.0420
  1-4 NB = 5539.6651 1-4 EEL = 23290.4390 VDWAALS = -3500.2889
  EELEC = -35909.3325 EGB = -5600.9507 RESTRAINT = 0.0000
  ESURF = 96.6693
  ------------------------------------------------------------------------------

The simulation then crashes with

      Coordinate resetting (SHAKE) cannot be accomplished,
      deviation is too large
      NITER, NIT, LL, I and J are : 0 5 2298 4623 4624

      Note: This is usually a symptom of some deeper
      problem with the energetics of the system.

You can see the total energy and total kinetic energy jump
dramatically over a 100 ns interval and the temperature jumps to >
500K. I would expect something like this if this was early in the
simulation and there were some kind of structural problem with the
initial model, but after 50000 steps???

Anyone have any suggestions as to what might be happening?

Thanks,
--Randy