[gmx-users] crash due to huge files using reaction field
Robert d'Rozario
ROZARIO at biop.ox.ac.uk
Tue Jan 11 19:56:19 CET 2005
Hi,
Where exactly is this water molecule? Is it in the bulk or close to the
protein?
Rob
On Tue, 11 Jan 2005 hverli at cbiot.ufrgs.br wrote:
> 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
>
--------------------------------------------------------------------
Centro de Biotecnologia da Universidade Federal do Rio Grande do Sul
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