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

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

>
>
> 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.

> -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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