[gmx-users] mdrun_mpi segmentation fault for run in vacuum

[reisingere at rostlab.informatik.tu-muenchen.de]

>
>
> On 6/12/12 5:54 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I tried to run a minimization just of the hydrogen of a membrane
>> protein.
>> I want to do this in vacuum.
>>
>> But when I started the run with
>>
>> mpirun mdrun_mpi -deffnm protein -v -nt 2
>>
>> I get the error that there is a segmentation fault.
>
> Threading and MPI parallelization are independent.  You can't use both.
> If
> you've compiled with MPI support, you can't invoke the -nt option.

okey, I'll try it without the -nt option. But I still get the error
>
>> But when I only type
>>
>> mpirun mdrun_mpi
>>
>> there is no problem so I guess that my already produced input files are
>> the problem. For example I am not completely sure about the .mdp file.
>> Can
>> you please give me an example for a .mdp file for a minimization of only
>> the hydrogen but not the whole protein in a vacuum.
>>
>
> It would be far more useful for you to post what you're using so we can
> provide


The .mpd file I use looks like this:

define          = -DPOSRES
integrator      = md
tinit           = 0
dt              = 0.005
nsteps          = 20000
nstxout         = 5000
nstvout         = 5000
nstfout         = 0
nstlog          = 1000
nstxtcout       = 1000
nstenergy       = 1000
energygrps      = Protein Non-Protein
nstcalcenergy   = 5
nstlist         = 5
ns-type         = Grid
pbc             = xyz
rlist           = 0.9
coulombtype     = Cut-off
rcoulomb        = 0.9
rvdw            = 0.9
fourierspacing  = 0.12
pme_order       = 4
ewald_rtol      = 1e-5
tcoupl          = V-rescale
tc-grps         = Protein  Non-Protein
tau_t           = 0.1      0.1
ref_t           = 298      298
Pcoupltype      = Isotropic
tau_p           = 2.0
compressibility = 4.5e-5
ref_p           = 1.0
gen_vel         = no
constraints     = all-bonds
constraint-algorithm = Lincs
unconstrained-start  = yes
lincs-order     = 4
lincs-iter      = 1
lincs-warnangle = 30
implicit_solvent = GBSA
gb_algorithm    = HCT
nstgbradii      = 1.0
rgbradii        = 0.9
gb_epsilon_solvent = 80
gb_dielectric_offset = 0.009
sa_algorithm    = Ace-approximation



> feedback.  The fact that the second command works while the first fails
> should
> lead to the opposite conclusion - your input is fine, but your invocation
> of
> mdrun was incorrect.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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