[gmx-users] "Segmentation fault" in mdrun

[Haberl Florian]

Hi,



> It has occuring an error in my simulation in
> vacuo. It appears as "segmentation fault"
> before completing the mdrun.
> In the archive md.log it has a LINCS WARNING and
> the following phrase: "Constraint error in
> algorithm Lincs at step -1". But I'm not using
> constraint, as you could see below.
>
> The em and md.mdp I'm using are as follows.
>
Do you get this error in em or md simulation?


> em.mdp
>
> cpp                 =  /lib/cpp
> define              =  -DPOSRES -DFLEX_SPC

You define here -DPOSRES, this is also position restraining.

take a look at
http://www.gromacs.org/documentation/reference_3.2/online/mdp_opt.html

search for -DPOSRES


> constraints         =  none
> integrator          =  steep
> nsteps              =  10000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100
> emstep              =  0.00001
>
> nstcomm             =  1
> ns_type             =  grid
> rlist               =  1.5
> rcoulomb            =  1.5
> rvdw                =  1.5
> Tcoupl              =  no
> Pcoupl              =  no
> gen_vel             =  no
>
>
> md.mdp
>
>
> define                   = -DFLEX_SPC
> constraints              = none
> integrator               = md
> dt                       = 0.002
> tinit                    = 0
> nsteps                   = 25000 ; 50 ps
> simulation
> comm_mode                = linear
> nstcomm                  = 1
> comm_grps                = Protein  MKC
>
>
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1
> rcoulomb_switch          = 0
> rcoulomb                 = 0.9
> epsilon_r                = 1
> vdwtype                  = Switch
> rvdw_switch              = 0
> rvdw                     = 0.9
>
>
> coulombtype              = Switch
> pme_order                = 6
> optimize_fft             = yes
>
>
> tcoupl                   = Berendsen
> tc-grps                  = Protein  MKC
> tau_t                    = 0.1      0.1
> ref_t                    = 300      300
>
>
> nstxout                  = 500
> nstvout                  = 0
> nstlog                   = 10
> nstenergy                = 10
> nstxtcout                = 0
> energygrps               = Protein  MKC
>
>
> gen_vel                  = yes
> gen_temp                 = 300
> gen_seed                 = 173529
>


Greetings,

Florian

------------------------------------------------------------------------
 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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