[gmx-users] version 3.3 - Range checking error
Yang Ye
leafyoung81-group at yahoo.com
Mon Nov 28 16:55:03 CET 2005
Joanne Hanna wrote:
>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.
>
>
and another equilibration with pcoupl?
>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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--
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/
--
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/
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