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

[Justin A. Lemkul]

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.

-Justin

-- 
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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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