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

[Steffen Haerterich]

Hi
in my first MDs with Gromacs I had a very similar expierience. I got 
LINCS-Warnings and after some time these increased until the run 
crashed. (The log-file filledmy harddisk and mdrun got stuck)
Now everything is stable and I don't really know the reason why. I think 
that I changed something in the .mdp but later tests to get to know 
what had caused the error were without results. The error did not occur 
anymore, even with the same parameters as before.
I fear that I am not of any help to you. I can only give some hope that 
there is a solution.

Good Luck,
Steffen

On 11 Jan 2005 at 16:46, 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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> > >
> > >
> > > --------------------------------------------------------------------
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> >
> 
> 
> 
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