AMBER Archive (2003)

Subject: AMBER: SHAKE Problem

From: Richard Smith (dicksmit_at_umich.edu)
Date: Wed Aug 06 2003 - 15:02:30 CDT

Hi

   I am using sander_classic of AMBER6 to equilibrate a protein in an
octahedral box of TIP3P water. I am using periodic boundary conditions
with constant pressure to increase the temperature from 50 - 310K in 50
K increments at 10 ps each with a 0.002 ps time step (the last increase
is from 250 to 310 K). Prior to this ramping I had performed the same
temperature ramping on the water molecules and equilibrated for 200 ps
allowing only the water to move. However, 4.322 ps into the last
interval heating of the entire system I receive the following error:
        
COORDINATE RESETTING (SHAKE) WAS NOT ACCOMPLISHED
     WITHIN 3000 ITERATIONS

      A V E R A G E S O V E R 2161 S T E P S

 NSTEP = 2161 TIME(PS) = 294.322 TEMP(K) = nan PRESS =
-82.70
 Etot = nan EKtot = nan EPtot =
-106819.0387
 BOND = 864.5095 ANGLE = 2330.2731 DIHED =
1790.9342
 1-4 NB = 1078.4580 1-4 EEL = 13450.7007 VDWAALS =
11680.7563
 EELEC = -138014.6706 EHBOND = 0.0000 CONSTRAINT =
0.0000
 EKCMT = 9078.0611 VIRIAL = 9825.4987 VOLUME =
420416.5997
                                                Density =
0.8429
 
------------------------------------------------------------------------
------

      R M S F L U C T U A T I O N S

 NSTEP = 2161 TIME(PS) = 294.322 TEMP(K) = nan PRESS =
338.52
 Etot = nan EKtot = nan EPtot =
1990.3060
 BOND = 41.7380 ANGLE = 86.6224 DIHED =
29.6364
 1-4 NB = 15.5528 1-4 EEL = 40.5114 VDWAALS =
788.8323
 EELEC = 2406.1291 EHBOND = 0.0000 CONSTRAINT =
0.0000
 EKCMT = 372.6604 VIRIAL = 2984.6189 VOLUME =
11762.7535
                                                Density =
0.0238
 
------------------------------------------------------------------------
------

 FATAL ERROR

  When I look at the system just before it crashes, one of the 12 sodium
counter-ions is right on the edge of the box of water. I tried to
increase the box size to try and keep the ion in the box but the error
still occurs around the same time into the simulation. I also tried
minimizing the structure obtained just before the FATAL ERROR for 100
steps with sander_classic and then performing the ramping to try and
relieve any bad contacts that could be causing this, but again I receive
the same error. I then tried decreasing the time step to 0.001 ps, but
I receive the same error. I have tried increasing the temperature even
slower, (20 K increments from 10K - 310K at 10 ps on each interval) with
both a 0.002 ps time step and a 0.001 ps time step, but the same error
occurs. Each time the ion ends up right on the edge of the box. With
the periodic boundary and the octahedral box, is there a problem with a
sodium atom leaving the box, which could lead to this problem?
Shouldn't the sodium ion reappear on the other side of the box, since
periodic boundary conditions are used?

Thank you for your help on this item and previous questions I have posed
on the Reflector,

Richard Smith

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