[gmx-users] segmentation fault

[Mark Abraham]

On 15/01/2011 8:50 PM, leila separdar wrote:
> I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard 
> Jones potential in a cubic box with linear size of 3.34. but when I 
> reduced units I confront with this error
> Back Off! I just backed up md.log to ./#md.log.5#
> Reading file argon.tpr, VERSION 4.0.7 (single precision)
>
> Back Off! I just backed up argon.trr to ./#argon.trr.3#
>
> Back Off! I just backed up ener.edr to ./#ener.edr.3#
> starting mdrun 'Built with Packmol'
> 1000000 steps,   1000.0 ps.
> Segmentation fault

What was your command line? What does the end of the logfile say? Why 
are you using PME for an LJ simulation that presumably has no 
electrostatic interactions?

Mark

>
> there is no error in energy minimization or grommp command. could u 
> please help me?
> here is my md.out file iin reduced units.
> cpp                 = /usr/bin/cpp
> integrator          = md
> dt                  = 0.001
> nsteps              = 1000000
> nstcomm             = 100
> nstxout             = 100
> nstvout             = 100
> nstfout             = 0
> nstlog              = 100
> nstenergy           = 100
> nstlist             = 10
> ns_type             = grid
> rlist               = 2.9
> coulombtype         = PME
> rcoulomb            = 2.9
> rvdw                = 2.9
> fourierspacing      = 0.35
> fourier_nx          = 0
> fourier_ny          = 0
> fourier_nz          = 0
> pme_order           = 4
> ewald_rtol          = 1e-5
> optimize_fft        = yes
>
> ;Berendsen temperature coupling is on in three groups
> Tcoupl             = berendsen
> tau_t              = 0.1
> tc_grps            = GAS
> ref_t              = 2.5
>
> ;generate velocities
> gen_vel            = yes
> gen_temp            = 2.5
> gen_seed           = 173529