[gmx-users] crash due to huge files using reaction field

[hverli at cbiot.ufrgs.br]

Hi,

I observed more carefully the .log file produced. The abnormal behaviour starts
to be observed with the following error:

Constraint error in algorithm Lincs at step 6007

t = 4012.014 ps: Water molecule starting at atom 22166 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous
and current coordinates

Step 6008  Warning: pressure scaling more than 1%, mu: -48.3359 -48.3359
-48.3359

Step 6008, time 4012.02 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
max 30417.687500 (between atoms 1331 and 1333) rms 1830.933472
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
      1      2   87.7    1.4805   1.7950      0.1000
   1319   1321   89.2    2.0797   1.2071      0.1250
   1322   1323  110.0   28.9309 114.1518      0.1230
   1324   1326   36.2  222.3204 1418.0717      0.1470
   1326   1327   47.9  313.1648 1373.9336      0.1530
   1326   1331  167.6  1177.7128 3305.2888      0.1530
   1331   1332  176.8  1265.0084 2938.6851      0.1230
   1331   1333  168.6  832.0464 4045.6855      0.1330
   1333   1334  168.5  813.7875 2697.6504      0.1000
   1333   1335  171.8  502.3141 3750.8442      0.1470
   1335   1336  163.5  937.9169 2604.0337      0.1530
   1335   1348  170.7  1498.6737 3003.0903      0.1530
   1336   1337   73.9   79.6411 890.5843      0.1530
   1337   1338   58.7   35.8450  34.7092      0.1530

But this error does not stop the simulation. Instead of it the following
messages appear:

Constraint error in algorithm Lincs at step 6008
Correcting invalid box:
old box (3x3):
   old box[    0]={-5.34475e+03,  0.00000e+00, -0.00000e+00}
   old box[    1]={ 0.00000e+00, -5.34475e+03, -0.00000e+00}
   old box[    2]={ 0.00000e+00,  0.00000e+00, -5.34475e+03}
new box (3x3):
   new box[    0]={-5.34475e+03,  0.00000e+00, -0.00000e+00}
   new box[    1]={ 0.00000e+00, -5.34475e+03, -0.00000e+00}
   new box[    2]={ 0.00000e+00,  5.34475e+03, -5.34475e+03}

and continues in a infinite loop, originating the huge size of the file, I
suppose.

When the error occurs,  the simulation was at approximatelly 4.0ns, and the
system was until than quite stable. So what could be the reason for such error?

Thanks,

Hugo.

> On Tue, 2005-01-11 at 13:12 -0200, hverli at cbiot.ufrgs.br wrote:
> > Hi, David,
> >
> > due to the size of the file I was not able to see it.
> then make it smaller with simple unix tools, like head.
> >
> > Hugo.
> >
> > > On Tue, 2005-01-11 at 11:30 -0200, hverli at cbiot.ufrgs.br wrote:
> > > > Hi,
> > > >
> > > > I have been experiencing some strange problems with reaction field. In
> two
> > > > different protein systems with about ~120 aminoacids each one
> (including
> > > water
> > > > and ions), at some point of the simulations (~4.0ns) gromacs generated
> a
> > > huge
> > > > .log file (>60GB!), completely filling the hard disk and so stopping
> the
> > > > simulation. We tried to simulate those systems in other machines,
> > > considering a
> > > > hardware problem, but the error still occurs (approximately in the same
> > > time
> > > > step). We are using the Mandrake linux, and so considering a possible
> > > problem
> > > > with the operational system we simulated in both Makdrake 9.2 and 10.0,
> and
> > > > again the error was observed. It appears to be quite reproducible.
> > > What's in the log file?
> > >
> > > --
> > > David.
> > > ________________________________________________________________________
> > > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> > > Dept. of Cell and Molecular Biology, Uppsala University.
> > > Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > > phone:  46 18 471 4205          fax: 46 18 511 755
> > > spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >
> > >
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> > Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul
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