[gmx-users] Grompp failed under double precision

Jack Shultz js at drugdiscoveryathome.com
Mon Dec 7 19:38:17 CET 2009

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 ]


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
> 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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