[gmx-users] version 3.3 - Range checking error

Mon Nov 28 11:11:16 CET 2005

Yes I have compared the tprs (see previous post)
The email from david said it might be useful to do what i have just reported so I have done so.
I don't think there is something wrong with my system as it runs in single precision in both v3.2.1 and v3.3 without this error.
And my pressure coupling looks pretty good. I have also  already run for 500ps without pressure coupling to equilibriate my water.

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk
>>> leafyoung81-group at yahoo.com 11/28/05 08:09 AM >>>
Hi

>The output from the single precision tpr with mdrun_d in gmx 3.3 is as follows;
>  
>
...

>this message was given in my pbs  output file after 115ps of simulation.
>
>Does this help pinpont the problem?
>  
>
No. What you have done is actually a waste of space, frankly. Have you 
used gmxcheck -f1 single.tpr -f2 double.tpr to compare them as David says?

I got such error as well, usually caused by improper pressure coupling. 
By turn pcoul off, I can continue running it. In your case, try to 
equilibrate more.

Yang Ye

Joanne Hanna wrote:

>Thanks
>Jo
>
>
>
>Joanne Hanna
>Department of Chemistry
>University of Warwick
>Coventry
>CV4 7AL
>
>J.F.Hanna at warwick.ac.uk
>  
>
>>>>spoel at xray.bmc.uu.se 11/25/05 10:39 AM >>>
>>>>        
>>>>
>Joanne Hanna wrote:
>
>  
>
>>Hello
>>
>>What I did was to use the files that were the output from a posres md 500ps run in v 3.2.1 (posres on protein, truc oct box spc water) and do grompp_d with v 3.3 and then mdrun_d with v3.3
>> 
>>
>>    
>>
>Please compare the single and double precision tpr files using gmxcheck. 
>In addition try to reproduce the problem by using the single precision 
>tpr file with mdrun_d. If the tpr files are different there may be a 
>problem with grompp, if they are identical there may be a problem with 
>mdrun_d. Either way it is necessary to find out what is going on. If you 
>can pinpoint the problem please submit a bugzilla.
>
>  
>
>>The hardware and os details are:
>>
>>Altix
>>node type: 1 x 1.6 GHz Itanium2 56-way SMP
>>interconnect: SGI NUMAlink4
>>OS: RedHat Enterprise Linux AS 3.0 / SGI ProPack
>>
>>All code was compiled with:
>>intel-cc-9/9.0.026
>>intel-fc-9/9.0.028
>>using lmpi
>>and enable threads for fftw
>>
>>I compiled fftw v 3 with the flags below, as there were no default flags for the intel compilers:
>>export CFLAGS="-ftz -O3 -tpp2 -no-gcc"
>>export FFLAGS="-ftz -O3 -tpp2"
>>
>>The only messages i got during during gromacs v3.3 compilation that i was unsure about are:
>>
>>checking dynamic linker characteristics... ifort: Command line warning: ignoring option '-p'; no argument required
>>ifort: Command line error: no files specified; for help type "ifort -help"
>>
>>mknb_innerloop.c(362): warning #188: enumerated type mixed with another type
>>                        mknb_func.coul=coulsave;
>>                                      ^
>>mknb_innerloop.c(363): warning #188: enumerated type mixed with another type
>>                        mknb_func.vdw=vdwsave;
>>                                     ^
>>Hope this is what you were asking
>>
>>Jo
>>
>>
>>
>>Joanne Hanna
>>Department of Chemistry
>>University of Warwick
>>Coventry
>>CV4 7AL
>>
>>J.F.Hanna at warwick.ac.uk
>> 
>>
>>    
>>
>>>>>spoel at xray.bmc.uu.se 11/25/05 10:02 AM >>>
>>>>>       
>>>>>
>>>>>          
>>>>>
>>Joanne Hanna wrote:
>>
>> 
>>
>>    
>>
>>>Hello
>>>
>>>I have recently tried to re run a simualtion with gromacs v3.3 in double precision that I have managed to run in v3.2.1 single prescision and v3.3 single precision. This simulations is failing with the following error:
>>>
>>>
>>>   
>>>
>>>      
>>>
>>Is this run with the same tpr file that works in single precision?
>>
>>What kind of hardware do you run on?
>>
>> 
>>
>>    
>>
>>>*******************************************************
>>>
>>>         Step           Time         Lambda
>>>       104000      208.00000        0.00000
>>>
>>> Energies (kJ/mol)
>>>     G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
>>>  8.43377e+03    3.79108e+03    2.53005e+03    3.13091e+02    5.79138e+04
>>>      LJ (SR)   Coulomb (SR)   Coul. recip.      Potential    Kinetic En.
>>>  1.38869e+05   -1.05323e+06   -1.68330e+05   -1.00971e+06    1.91922e+05
>>> Total Energy    Temperature Pressure (bar)
>>> -8.17790e+05    3.11754e+02    4.49698e+01
>>>
>>>-------------------------------------------------------
>>>Program mdrun_d, VERSION 3.3
>>>Source code file: nsgrid.c, line: 226
>>>
>>>Range checking error:
>>>Explanation: During neighborsearching, we assign each particle to a grid
>>>based on its coordinates. If your system contains collisions or parameter
>>>errors that give particles very high velocities you might end up with some
>>>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
>>>put these on a grid, so this is usually where we detect those errors.
>>>Make sure your system is properly energy-minimized and that the potential
>>>energy seems reasonable before trying again.
>>>
>>>Variable ci has value 5926. It should have been within [ 0 .. 5760 ]
>>>Please report this to the mailing list (gmx-users at gromacs.org)
>>>-------------------------------------------------------
>>>
>>>"Clickety Clickety Click" (System Manager From Hell)
>>>
>>>*******************************************************
>>>
>>>Could anyone please explain to me what I have done wrong? Should I have re-do the entire process with the double preision? i.e. from starting structure, solvate minimise, md with posres on protein to equilib water and then run my simualtion?
>>>
>>>Many thanks
>>>Jo
>>>
>>>Joanne Hanna
>>>Department of Chemistry
>>>University of Warwick
>>>Coventry
>>>CV4 7AL
>>>
>>>J.F.Hanna at warwick.ac.uk
>>>_______________________________________________
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>>>
>>>   
>>>
>>>      
>>>
>> 
>>
>>    
>>
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>  
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-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/

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