[gmx-users] help me (Fatal error: ci = -2147483648 should be in 0 .. 12166 [FILE nsgrid.c, LINE 210]

[David]

On Wed, 2003-12-03 at 03:58, Mauricio Arenas Salinas wrote:
> hi all:
> 
> I am trying to run a Md of a protein but she throws the 
> following error:
> Back Off! I just backed up traj.xtc to ./#traj.xtc.3#
> Fatal error: ci = -2147483648 should be in 0 .. 12166 
> [FILE nsgrid.c, LINE 210]
> that it means?  and as I can solve it? 
> this it is my file of md.mdp:
> '


is your structure energy minimized?

bad structures can cause all these problems, and even SEGV. We don't
check for them because of efficiency.

> cpp = /lib/cpp
> include = -I../top
> ;constraints = all-bonds
> integrator = md
> dt = 0.001
> nsteps = 1000 ; 1 ps
> nstcomm        = 1
> ; collect data every  ps
> nstxout = 5000
> nstvout = 0
> nstfout = 0
> nstlog = 0
> nstenergy = 250
> nstxtcout = 250
> xtc_grps = Protein 
> energygrps = Protein Sol
> nstlist = 10
> ns_type = grid
> pbc: xyz
> rlist = 0.8
> coulombtype = PME
> rcoulomb = 0.8
> pme_order      = 4
> fourierspacing = 0.12
> fourier_nx     = 0
> fourier_ny     = 0
> fourier_nz     = 0 
> rvdw           = 0.8
> ewald_rtol     = 1e-5
> optimize_fft   = no
> ; Berendsen temperature coupling is on in two groups
> tcoupl = Berendsen
> tc-grps = Protein Sol 
> tau_t = 0.1 0.1
> ref_t = 300 300
> ; Pressure coupling is on
> Pcoupl = no
> tau_p = 1.0
> ref_p = 1.0
> ; Generate velocites is on at 300 K.
> gen_vel = no
> 
> thank you very much.
> 
> 
> "El alto invierno besa tu armadura 
> y te cubre de labios destruidos:
> la primavera de violento aroma 
> rompe su sed en tu implacable estatua:
> y el grave otoño espera inútilmente 
> derramar oro en tu estatura verde."
> 
> ARAUCARIA, PABLO NERUDA
> 
>   
> 
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
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