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
Received on Thu Sep 19 2002 - 13:51:28 PDT
