RE : [gmx-users] segmentation fault in mdrun when using PME

[Diane Fournier]

________________________________

De: gmx-users-bounces at gromacs.org de la part de David van der Spoel
Date: lun. 2006-05-01 13:33
À: Discussion list for GROMACS users
Objet : Re: [gmx-users] segmentation fault in mdrun when using PME




Have you enabled fortran at the compilation stage? In that case try it
without, otherwise please file a bugzilla, such that we can document
this problem (and try to fix it of course).

>Still doesn't work. logfile ends in the usual way. Except this time, I get this output:
>

Reading file trp_em.tpr, VERSION 3.3.1 (single precision)

Steepest Descents:

Tolerance (Fmax) = 1.00000e+03

Number of steps = 500

Warning: 1-4 interaction between 1 and 7 at distance 39513.957 which is larger than the 1-4 table size 1.000 nm

These are ignored for the rest of the simulation

This usually means your system is exploding,

if not, you should increase table-extension in your mdp file

Wrote pdb files with previous and current coordinates

Back Off! I just backed up step0.pdb to ./#step0.pdb.1#

Wrote pdb files with previous and current coordinates

and then these files get written:

step0.pdb

#step0.pdb.1# 

step-1.pdb 

step1.pdb 

Will file a bugzilla.
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://folding.bmc.uu.se
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