AMBER Archive (2002)

Subject: van der Waals explosion

From: Arvid Soederhaell (arvid_at_fmp-berlin.de)
Date: Fri Jun 21 2002 - 03:54:05 CDT

Dear all

This is a continuation of my SHAKE problems, for those who have followed
the story...
The situaiton is the following:
I can simulate the membrane without SHAKE using a timestep of 0.2 fs. It
has been stable for 100 ps. After that equilibration, i switch on SHAKE
and use a 2 fs timestep. (The membrane has now a relatively stable area
and density) After another almost 95.000 steps i get the message

#####################################################################

 NSTEP = 94600 TIME(PS) = 4553.950 TEMP(K) = 325.61 PRESS = 63.57
 Etot = -10848.0153 EKtot = 9815.6357 EPtot = -20663.6510
 BOND = 1095.9350 ANGLE = 4186.8751 DIHED = 1017.8010
 1-4 NB = 1483.5495 1-4 EEL = 355.9833 VDWAALS = -1876.0503
 EELEC = -26927.7446 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 1793.8733 VIRIAL = 1615.0149 VOLUME = 130318.1206
 T_SOLUTE = 325.3978 T_SOLVENT = 326.0009
                                                Density = 1.0003

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

 NB-update: NPAIRS = 7572088 HBPAIR = 642524
 NB-update: NPAIRS = 7568802 HBPAIR = 640884

     COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
     DEVIATION IS TOO LARGE
     NITER, NIT, LL, I AND J ARE : 0 0 4609 7494 7495

##################################################################

which is the usual when SHAKE crashes. In order to investigate exactly
what is happening, I restart the simulation, now without SHAKE and a
timestep of 1 fs. (Normally C-H bonds should be possible to integrate
using this timestep, or?) This simulaiton runs for 64 steps and then it
starts to explode. (Since i don't use SHAKE now, the simulation is not
terminated, and i can follow the explosion a short while.) The output is
the following:

#########################################################################

NSTEP = 62 TIME(PS) = 4554.012 TEMP(K) = 268.39 PRESS = 1121.28
 Etot = -9662.1812 EKtot = 10856.0729 EPtot = -20518.2542
 BOND = 2069.4952 ANGLE = 4286.7684 DIHED = 1038.0870
 1-4 NB = 1480.2171 1-4 EEL = 344.6148 VDWAALS = -1199.2859
 EELEC = -28538.1508 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 1902.8618 VIRIAL = -1238.1350 VOLUME = 129740.8907
 T_SOLUTE = 272.0556 T_SOLVENT = 262.5738
                                                Density = 1.0048

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

 NSTEP = 63 TIME(PS) = 4554.013 TEMP(K) = 272.68 PRESS = 1041.92
 Etot = -9733.4034 EKtot = 11029.7825 EPtot = -20763.1859
 BOND = 1887.3813 ANGLE = 4273.8634 DIHED = 1037.2499
 1-4 NB = 1482.6949 1-4 EEL = 346.9935 VDWAALS = -1197.1443
 EELEC = -28594.2246 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 1903.8994 VIRIAL = -1015.2951 VOLUME = 129762.4987
 T_SOLUTE = 272.9961 T_SOLVENT = 272.1836
                                                Density = 1.0046

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

 NSTEP = 64 TIME(PS) = 4554.014 TEMP(K) =********* PRESS =2219470.07
 Etot = ************ EKtot = ************ EPtot = 305191.6644
 BOND = 2059.3977 ANGLE = 4244.1121 DIHED = 1035.5665
 1-4 NB = 1484.7063 1-4 EEL = 349.6737 VDWAALS = 324912.0046
 EELEC = -28893.7964 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 1904.3927 VIRIAL = ************ VOLUME = 129782.5794
 T_SOLUTE =*********** T_SOLVENT = 283.2194
                                                Density = 1.0045

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

 NSTEP = 65 TIME(PS) = 4554.015 TEMP(K) =********* PRESS =**********
 Etot = ************ EKtot = ************ EPtot = ************
 BOND = ************ ANGLE = 5376.6749 DIHED = 1040.3525
 1-4 NB = 1483.4146 1-4 EEL = 353.8324 VDWAALS = ************
 EELEC = -23224.5772 EHBOND = 0.0000 CONSTRAINT = 0.0000
 EKCMT = 8136470.0316 VIRIAL = ************ VOLUME = 162081.8670
 T_SOLUTE =*********** T_SOLVENT = 295.9947
                                                Density = 0.8043

------------------------------------------------------------------------------
##############################################################################

As you can see the VDWAALS energy increases dramatically between step 63
and 64.
Now I take a closer look at the trajectory and monitor the distances
between the C and H in one of the exploding CH3 groups (methyl, end of
one of the lipid tails) and the distance to the adjacent bonded CH2 group:

step: CH CH CH to next CH2 grp (C-C)
59 1.09 1.08 1.11 1.56
60 1.10 1.10 1.11 1.56
61 1.11 1.11 1.11 1.56
62 1.11 1.12 1.10 1.56
63 1.11 1.12 1.09 1.56
64 1058.88 486.67 2.28 2.81

Moreover there is no non bonded group close to this particular CH3 group
in step 60-64.

To me this doesn't really look like a vdW exploison since the distances
are never too short, which is normally the case. The atom types in the CH3
group are CT for the carbon and HC for the hydrogens, the charges
are -0.101590 for the carbon and 0.033863 for the 3 hydrogens. (Net
charge 0.)

Any suggestion to what might cause the troubble is just as welcome as a
second chance for Sweden against Zenegal in the soccer world
championship....

Arvid