[gmx-users] Grompp failed under double precision

[Mark Abraham]

Jack Shultz wrote:
> this issue was resolved by using the non-standard spce.itp provided by
> acpypi. But I have a little problem still running in double precision
> 
> 
> Run this script up to the point of minimization and it works.
> 
> 
> grompp -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr
> 
> mdrun -v -deffnm em
> 
> however...when I use double precision
> 
> grompp_d -f em.mdp -c Complex_b4em.pdb -p Complex.top -o em.tpr
> mdrun_d -v -deffnm em
> 
> 
> Back Off! I just backed up em.log to ./#em.log.2#
> Getting Loaded...
> Reading file em.tpr, VERSION 4.0.5 (double precision)
> Loaded with Money
> 
> 
> Back Off! I just backed up em.trr to ./#em.trr.2#
> 
> Back Off! I just backed up em.edr to ./#em.edr.2#
> Polak-Ribiere Conjugate Gradients:
>   Tolerance (Fmax)   =  1.00000e+02
>   Number of steps    =          200
>   F-max             =          inf on atom 3
>   F-Norm            =          inf
> 
> 
> -------------------------------------------------------
> Program mdrun_d, VERSION 4.0.5
> Source code file: nsgrid.c, line: 357
> 
> 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 -2147483648. It should have been within [ 0 .. 1540 ]
> 
> -------------------------------------------------------

Well that makes almost no sense at all! It is just possible that the 
above behaviour is reasonable for a system close to the edge of a 
numerically unstable EM. Look closely at the starting structure for 
clashing atoms and such like. Try generating it another way, using 
another simulation system entirely, etc.

If none of the above helps, and you can reproduce this in two different 
directories with separate files from clean installs of unmodified 
GROMACS 4.0.5 then you may have uncovered a bug. If so, please lodge a 
Bugzilla on the GROMACS website, describing your hardware, how you built 
GROMACS, and attaching tarballs of inputs and outputs.

Mark

> On Sun, Dec 6, 2009 at 7:43 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> Jack Shultz wrote:
>>> We have a workflow going, and I switched to double precision because
>>> of the LINCS issues. I got this error now with grompp. I don't think
>>> anything else is different other than double precision, but I included
>>> the logs for this.
>>>
>>> -------------------------------------------------------
>>> Program grompp_d, VERSION 4.0.5
>>> Source code file: toppush.c, line: 1273
>>>
>>> Fatal error:
>>> [ file spce.itp, line 32 ]:
>>> Atom index (1) in bonds out of bounds (1-0).
>>> This probably means that you have inserted topology section "bonds"
>>> in a part belonging to a different molecule than you intended to.
>>> In that case move the "bonds" section to the right molecule.
>>> -------------------------------------------------------
>>>
>> Please see the following:
>>
>> http://www.gromacs.org/Documentation/Errors#Atom_index_(1)_in_bonds_out_of_bounds
>>
>> Particularly of interest is the section within about the AMBER force fields,
>> for which the default spc.itp is incompatible.
>>
>> -Justin
>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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> 
> 
>