[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 16:09:26 CEST 2012
>
>
> On 6/12/12 8:48 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>>>
>>>
>>> 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?
>>
>
> Sure, it's possible, but perhaps you can clarify a few things, because
> there are
> a number of inconsistencies in what you've been saying.
>
> 1. EM and MD are different processes. If you want to minimize the
> position of
> only H atoms and keep others restrained, use the .mdp file I provided
> above. I
> doubt it will accomplish much though, since you're restraining a large
> part of
> the system.
>
> 2. I though you were working in vacuo? Where do you have explicit water?
> Is
> this some sort of droplet simulation? If it is, then using the infinite
> cutoff
> approach is probably not appropriate. There are a number of posts about
> such
> topics in the list archive and there is published literature in very good
> journals about how to do such simulations.
>
> The .mdp file below will be very inaccurate. Using a plain cutoff for
> Coulombic
> interactions is not appropriate with a finite value for rcoulomb. The
> .mdp file
> will also cause the program to run forever (with nsteps = -1), unless you
> kill
> it or something else does. You're also producing no output at all to a
> trajectory, energy file, or log file, so there's not much use in running
> MD
> forever just to get nothing. If you're trying to accomplish EM, then
> using the
> "md" integrator is incorrect, you need an EM algorithm.
I want to do two different things.
First I wanted to minimize the hydrogens of the protein, leave the rest of
the protein fix and do this in vacuum.
This already worked. Thank you!!
But now the next step is to run a md simulation with this minimized
structure. And again I only want to do the simulation for the hydrogens of
the protein and again in vacuum.
Eva
>
> -Justin
>
>> 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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>>
>>
>>
>
> --
> ========================================
>
> 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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