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 <[email protected]> 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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