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

[Attilio]

David van der Spoel wrote:

>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.
>
>  
>
I cheched my input file, and this is the section corresponding to the P 
coupling

 I;  P COUPLING
;
pcoupl              =  Parrinello-Rahman
compressibility     =  4.5e-5
tau_p               =  1.0
ref_p               =  1.0
pcoupltype          =  isotropic
;

I'm also using PME, with 1,2 cutoff.
I was thinking to increase the frequency of removal for the 
rototranslation of the center of mass of the system, or maybe I have to 
change some parameter for the lincs algotrithm  (that I applied only to 
h-bonds)?
Thanks
Attilio

>>"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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>>    
>>
>
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>

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