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

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

>
>
> On 6/12/12 7:34 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>>
>>>
>>> On 6/12/12 7:05 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>>>>
>>>>>
>>>>> 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
>>>>
>>>
>>> Your goal is energy minimization of H atoms in a vacuum, correct?  Your
>>> .mdp
>>> file is for a full MD simulation using an NVT ensemble in implicit
>>> solvent.
>>> What you want is something more along the lines of:
>>>
>>> define	    = -DPOSRES
>>> integrator  = steep
>>> emtol       = 1000.0
>>> emstep      = 0.01
>>> nsteps      = 50000
>>> energygrps  = system
>>> nstlist     = 1
>>> ns_type     = simple
>>> rlist       = 0
>>> coulombtype = cutoff
>>> rcoulomb    = 0
>>> rvdw        = 0
>>> pbc         = no
>>
>> but how does the minimization "know" that it should be in vacuum.
>
> There's nothing particularly special about running in vacuum except that
> there
> is no solvent.  Infinite cutoffs and a nonperiodic simulation cell are
> common
> conventions for simulating in vacuum, so that's what the .mdp file above
> does.

okey, thanks a lot!!
But when I want to do a whole md run after this minimization my first .mdp
file was correct, right?

>
> -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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