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

[Attilio]

Hi, it seems that the problems were the termostat and the barostat, I 
switched to berendsen and now the box remain cubic!

Attilio


Attilio wrote:

> Dear all,
>
> 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
> "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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