[gmx-users] water molecule not settled, is due to the change in the form of the box?

[David van der Spoel]

On Wed, 9 Feb 2005, Attilio wrote:

>I'm doing NPT md on my system, a small drug non covalently linked to 
>DNA, and I already performed 8.5 ns simulation.
>At this point I get this message

the problem is that you have selected anisotropic pressure scaling. You'll 
probably have to de redo the simulation with isotropic scaling. Do also 
consider to use PME with a cut-off of 0.9 nm, and 0.9/1.4 for the 
vanderwaals. It will be roughly equally fast and more accurate.

>
>"Inertia tensor (3x3):
>   Inertia tensor[    0]={ 4.61676e+03,  1.35627e+03, -2.24899e+03}
>   Inertia tensor[    1]={ 1.35627e+03,  8.25089e+03, -3.82382e+02}
>   Inertia tensor[    2]={-2.24899e+03, -3.82382e+02,  1.18415e+04}
>
>t = 8898.120 ps: Water molecule starting at atom 11315 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
>previous and current coordinates
>
>Step 5932081, time 8898.12 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>max 0.000000 (between atoms 1 and 2) rms nan
>bonds that rotated more than 30 degrees:
>atom 1 atom 2  angle  previous, current, constraint length
>
>t = 8898.121 ps: Water molecule starting at atom 11993 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
>previous and current coordinates
>
>Step 5932082, time 8898.12 (ps)  LINCS WARNING
>relative constraint deviation after LINCS:
>max 0.000000 (between atoms 1 and 2) rms nan
>bonds that rotated more than 30 degrees:
>atom 1 atom 2  angle  previous, current, constraint length
>
>t = 8898.123 ps: Water molecule starting at atom 11993 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
>previous and current coordinates
>....
>.....
>....
>
>t = 8898.141 ps: Water molecule starting at atom 11993 can not be settled.
>Check for bad contacts and/or reduce the timestep.Wrote pdb files with 
>previous and current coordinates
>Grid: -2147483648 x -2147483648 x -2147483648 cells
>Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]"
>
>
>I checked the simulation, and I see that the box, originally cubic, 
>transform to a rectangular box, so the minimum distance
>between the images decrease abruptly from 35 to 15 angtroms, and the DNA 
>strands separate (it's beatiful to see,
>not to report to your boss...).
>
>I'm using a time step of 1.5 ps, and a cutoff of 12 angstrom for both 
>electrostatic and van der waals.
>
>
>How may I go on without break my system?
>
>Thanks in advance,
>Attilio
>
>
>
>
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-- 
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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