[gmx-users] mdrun_mpi segmentation fault for run in vacuum
reisingere at rostlab.informatik.tu-muenchen.de
reisingere at rostlab.informatik.tu-muenchen.de
Tue Jun 12 14:48:49 CEST 2012
>
>
> On 6/12/12 7:46 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>>
>>>
>>> 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?
>>
>
> For running in implicit solvent, that .mdp file has a number of problems.
>
> By restraining the protein, you don't really accomplish anything. Also
> note
> that for using implicit solvent, you generally need infinite cutoffs (like
> in
> the case of the "vacuum" .mdp file I posted before) and no pressure
> coupling. I
> have found that with finite cutoffs, energy conservation is poor and
> structures
> are unstable when using implicit solvent.
>
> There are a number of useful discussions in the list archive about such
> considerations; I would encourage you to spend some time reading before
> diving
> headfirst into something that may not turn out well.
But when I want only the water atoms to be minimized and to run the md
simulation only for the water atoms I have to restrain the whole protein
or not? I already googled around a lot and I found many many examples for
.mdp files.
Is it possible to run an md simulation with the following .mpd file?
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.002 ; ps !
nsteps = -1
nstlist = 10
ns_type = grid
rlist = 1.0
coulombtype = cut-off
vdwtype = cut-off
rcoulomb = 1.0
rvdw = 1.0
pbc = no
epsilon_rf = 0
rgbradii = 1.0
comm_mode = angular
implicit_solvent = GBSA
gb_algorithm = HCT
gb_epsilon_solvent = 78.3
sa_surface_tension = 2.25936
nstxout = 0
nstfout = 0
nstvout = 0
nstxtcout = 0
nstlog = 0
nstcalcenergy = -1
nstenergy = 0
tcoupl = berendsen
tc-grps = system
tau-t = 0.1
ref-t = 300
Eva
>
> -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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