[gmx-users] neighborsearching in semiisotropic systems

[Till Rudack]

Dear Justin,
the system is well minimized. I performed a steepest descent 
minimization followed by a conjugate gradient minimization and then 
minimize it again with steepest descent. The problem occurred after 3ns 
or in the second run after 5ns so I do not think it is a problem of  
minimization .
Till

Justin A. Lemkul schrieb:
> Did you do any sort of minimization or equilibration on your system?  Usually
> these errors arise because of a poor starting structure, or one that has been
> insufficiently equilibrated.
>
> -Justin
>
> Quoting Till Rudack <till at bph.rub.de>:
>
>   
>> Dear users,
>>
>> During protein simulations occurred the range checking error of the
>> neighborsearching. I checked the comments on this mistake in the user
>> list and then checked my system on any hints of an exploding system but
>> it seems to be stable. In order to be sure I cut down the system to a
>> small peptide consisting of only ten aminoacids and used the ffG43a1
>> forcefield.
>>
>>
>> I performed 10ns simulations of this small system in a cubic
>> spc-waterbox with different pressure parameters and tried single and
>> double precision. I got the following results:
>>
>>
>> For
>>
>> pcoupltype = semiisotropic
>>
>> tau_p = 0.5 0.5
>>
>> compressibility = 4.5E-5 4.5E-5
>>
>> ref_p = 1 1
>>
>>
>> with double precision occurred the mistake:
>>
>>
>> -------------------------------------------------------
>>
>> Program mdrun_d.mpi, VERSION 3.3.1
>>
>> 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 284. It should have been within [ 0 .. 200 ]
>>
>> Please report this to the mailing list (gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>)
>>
>>
>> Then, I changed tau_p to 5.0 and the mistake did not occurce anymore
>> during the 10 ns. With single precision the mistake never occurres. I
>> also tested double precision with pcoupltype = isotropic and this also
>> works.
>>
>> Next, I wanted to reproduce the mistake so I took the same tpr file of
>> the crashed simulation with tau_p = 0.5 and started the simulation
>> again. The mistake occurred again but not at the same timestep. The
>> first run crashed after step 1558630 and the second run after step
>> 2597500 and also the ci variable is not exactly the same (Variable ci
>> has value 283. It should have been within [ 0 .. 200 ]).
>>
>>
>> I think there might be a problem between the neighborsearching and the
>> semiisotropic pressurcoupling together with double precision. I am quite
>> sure that the peptide is not the problem. Maybe there is a problem with
>> a water molecule. I would be glad if someone can give me an explanation
>> why this mistake is not reproducable at the same timestep and why it
>> occures with tau_p=0.5 and not with tau_p=5.0.
>>
>>
>> Thanks
>>
>>
>> Till
>>
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>>     
>
>
>
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul at vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
>
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