[gmx-users] segmentation fault

[leila separdar]

I managed to run my simulation but which kind of coulomtype can I use except
PME? also I get different averages for kinetic and potential energies than
before reducing units I think these numbers must be the same because
E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me
about this issue?( I have reduced box size, dt, C6=4 , C12=4, mass=1 and
temperature. before reducing temperature is 300 and after reducing it is
2.5)

On Sun, Jan 16, 2011 at 12:23 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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
>>
>
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