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

[Justin A. Lemkul]

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

-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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