[gmx-users] Segmentation Fault (Address not mapped)
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Aug 4 04:14:07 CEST 2009
Darrell Koskinen wrote:
> Hi Justin,
> I just want to use the most appropriate force field and associated
> parameters for my simulation of graphene in ammonia gas. Is OPLS an
> appropriate force field to use?
It seems fairly unlikely that it is appropriate. Force fields are
parameterized to reproduce a range of behaviour of a certain classes of
chemicals. To understand what these are, you need to read the primary
literature for that force field. There is no reason to suppose that a
force field parameterized to reproduce (say) condensed-phase properties
of peptides should be effective at modelling either infinite graphene,
or gas-phase ammonia. It might work, and similar things might have been
shown to work, but that's your job to prove and/or read about.
> I have searched for force fields for gas simulations but have not yet
> been able to find one specific to graphene and ammonia gas. Since
> graphene is in a condensed phase and ammonia is in a gas phase and I
> understand that I need to use the same force field for both graphene and
> ammonia, I will have to use a force field for either gas-phase MD or
> condensed-phase MD. Since I am finding it difficult to locate gas-phase
> MD force fields, is it acceptable to use a condensed-phase MD force
> field, which I believe is the case for OPLS (please confirm)?
Only if you can demonstrate that it's doing a good job. For starters,
does a simulation of gas-phase ammonia using these parameters reproduce
density and diffusion constants? Is an infinite graphene lattice in
vacuum stable? Otherwise any paper you wrote might be rejected out-of-hand.
> If it is acceptable to use OPLS, then I am assuming that I am to use the
> parameters in the ffoplsaabon.itp and ffoplsaanb.itp as is and not
> modify them (i.e. not create frankenstein force fields), correct? Am I
> correct in my understanding that the only item that requires
> modification is the .n2t file?
I can't say.
> And, by the way, I have resolved the segmentation fault problem. It was
> being caused by the freezing of the graphene lattice. When I removed the
> freezing, I saw the graphene structure curl upward and am thinking that
> by freezing the atoms in place it was creating great forces between the
> atoms as they were kept from moving into their preferred orientation.
Yep, that's right. The segfault was probably indirectly a consequence of
integrating large opposing forces on these atoms. A small perturbation
in a position might now result in a large change in net force, a large
displacement on a frozen atom, and the whole thing goes up in
silicaceous smoke.
> I subsequently tried to restrain the atoms via position restraints, but
> I still see the graphene structure moving. Could you please let me know
> why the position restraints do not appear to be working? Do I need to
> use greater restraint parameters? I created a position restaint file for
Yes and no. Position restraints are good for giving things a gentle
nudge to stay where you've put them. The textbook usage is that while
equilibrating a starting structure into an ensemble, you don't want it
to move much. Then once you're happy with your equilibrium ensemble,
then you remove the restraints and see what really happens. However, if
you're using them to smash something flat that really doesn't want to be
flat, then you run the risk of integration problems as above. The fact
of not wanting to be flat indicates that the model physics is severely
broken, as Dallas has observed. You need to work out how and why it is
broken, and once you fix the real problem, restraints or freezing might
not prove to be needed.
Mark
> the graphene structure posre.itp using "genpr -f graphene.gro -n
> index.ndx -o posre.itp -fc 0 0 1000" (note that genrestr is not
> recognized in my version of GROMACS) to restrain the graphene lattice to
> the x-y plane and submitted 2 runs with the following in my run.mdp file:
>
> Run 1:
> define =-DPOSRES
> constraints =none
>
> Run 2:
> define =-DPOSRES
> constraints =all-bonds
>
> Run 1 with constraints=none appears to restrain the graphene lattice
> better than the Run 2 with constraints=all-bonds.
>
> Here is an extract from posre.itp for the first few atoms:
>
> ******************************************
> ; position restraints for Grph of Ãzú^K^Q+
>
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 0 0 1000
> 2 1 0 0 1000
> 3 1 0 0 1000
> ******************************************
>
> Again, I thank you very much for your assistance.
>
> Darrell
>
>> Date: Mon, 27 Jul 2009 17:48:02 -0400
>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4A6E2092.402 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> Darrell Koskinen wrote:
>>
>>> Hi Justin,
>>> With regard to your comment about using other force fields for my
>>> simulation of graphene surrounded by ammonia gas, are referring to
>>> the force fields for both graphene and ammonia or only to the force
>>> field for graphene?
>>>
>>>
>>
>> The "force field" should be one in the same. The parameters should be
>> suitably derived using the same scheme as the original work.
>>
>>
>>> I reviewed my selection of the force field parameters for graphene
>>> and see that I selected the parameters from the paper by Cornell et
>>> al. since a paper on deformation of carbon nanotubes ("A structural
>>> mechanics approach for the analysis of carbon nanotubes" by Chunyu
>>> Li, Tsu-Wei Chou in International Journal of Solids and Structures 40
>>> (2003) 2487–2499) used parameters from the paper by Cornell et al. Is
>>> this sufficient to justify the use of these parameters? I also
>>> thought that graphene and ammonia would be considered organic since
>>> they are comprised of carbon, nitrogen, and hydrogen, which are all
>>> common elements found in organic matter.
>>>
>>>
>>
>> If you feel that precedent is sufficient, then I guess go ahead. But
>> realize that the paper by Cornell et al. refers to parameters suitable
>> for simulations of proteins and nucleic acids, as well as a few
>> organic functional groups. Parameterization was based on peptide
>> backbone geometry, as well as other parameters, likely none of which
>> involved graphene and gaseous ammonia (they were doing liquid
>> simulations).
>>
>>
>>> With regard to the parameters for ammonia, is it acceptable to use
>>> the parameters from the paper by Cornell et al. or do I need to find
>>> papers specifically related to ammonia gas molecular dynamics
>>> simulations?
>>>
>>>
>>
>> I would seriously consider finding parameters (if they exist) that
>> have been derived for use with gas-phase simulations.
>>
>>
>>> With regard to dihedral selection, I looked at the .top file and see
>>> that the function type is listed as 3 in the dihedrals section, which
>>> I believe indicates that my simulation is using a Ryckaert-Bellemans
>>> function. It appears to me that if I am using the OPLS force field
>>> that the Ryckaert-Bellemans dihedral type is automatically selected.
>>> I do see in the ffoplsaabon.itp file that there is an improper
>>> dihedral definition which think I could potentially use in my
>>> simulation "improper_Z_CA_X_Y", but how do I cause my simulation to
>>> use this definition? Do I need to add the following line to my .top
>>> file?
>>> "#define improper_Z_CA_X_Y"
>>>
>>>
>>
>> No, you would have to use a special dihedrals section, that specifies
>> the four atoms involved (function type 1), followed by the
>> specification of that particular improper ("improper_Z_CA_X_Y"). See
>> the manual for more details, and/or generate a topology for a protein
>> with pdb2gmx with OPLS-AA and see how they're defined.
>>
>>
>>> Further, I thought that I could simply modify the appropriate lines
>>> of the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters
>>> found in the paper by Cornell et al. so that they will be used in my
>>> simulation. Am I correct in my assumption?
>>>
>>>
>>
>> Modifying ffoplsaa files to parameters that are not OPLS-AA is
>> probably a bad choice. If you're dead-set on using these parameters,
>> download the ffamber ports and use the ffamber94 force field, not some
>> Frankensteined-OPLS. Besides, all of the parameters in the Cornell
>> paper are in kcal/mol/A^2, which will require conversion to Gromacs
>> standard units. If you've printed them directly in your previous
>> attempts, I can guarantee you you're not getting the values you think
>> you are.
>>
>> -Justin
>>
>>
>>> Thanks again for your help.
>>>
>>> Darrell
>>>
>>>
>>> >Date: Fri, 17 Jul 2009 22:11:07 -0400
>>> >From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >Message-ID: <4A612F3B.7060503 at vt.edu>
>>> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >
>>> >
>>> >
>>> >darrellk at ece.ubc.ca wrote:
>>> >> Hi Justin,
>>> >> I am using the ffoplsaabon.itp parameters for:
>>> >> bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3)
>>> >> angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H)
>>> >> dihedrals (X-CA-CA-X, X-CA-CT-X)
>>> >>
>>> >> I am using the ffolpsaanb.itp VdW parameters for H & N3
>>> >>
>>> >> And I am using the VdW parameters found in the paper "A Second
>>> >> Generation Force Field for the Simulation of Proteins, Nucleic
>>> Acids,
>>> >> and Organic Molecules" for CA, HA, CT, & HC doing the conversion
>>> from
>>> >> Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma
>>> and from
>>> >> kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for
>>> epsilon. The
>>> >> converted parameters for sigma were different by only +/-2% to +/-8%
>>> >> from the values in ffoplsaanb.itp, but the converted parameters for
>>> >> epsilon were different by +/-23% to +/-66% from the values in
>>> >> ffoplsaanb.itp. Is this a valid paper to use for selection of
>>> parameters?
>>> >>
>>> >
>>> >If memory serves, that paper is the derivation by Cornell, et al.
>>> for the
>>> >AMBER94 parameter set, so no, you are not going to find those same
>>> parameters in
>>> >ffoplsaanb.itp.
>>> >
>>> >Furthermore, the title of the paper indicates that the parameters
>>> are for
>>> >proteins, nucleic acids, and organic molecules. Has anyone else in the
>>> >literature used these parameters for graphene lattices? I would
>>> suggest using a
>>> >force field that others have used for such solid materials, like
>>> nanotubes or
>>> >other graphene surfaces. Otherwise, you will have to somehow
>>> demonstrate that a
>>> >force field designed for use with condensed phase biomolecules is
>>> applicable to
>>> >your gas-phase graphene lattice.
>>> >
>>> >> The graphene lattice is only vibrating slightly and looks like a
>>> bunch of
>>> >> travelling waves.
>>> >>
>>> >> I believe I am using proper dihedrals and not improper dihedrals
>>> in my
>>> >> model.
>>> >>
>>> >
>>> >It would seem. Consider if impropers might be necessary to keep
>>> your planar
>>> >groups planar. That's what they are there for.
>>> >
>>> >> Since the graphene structure will be connected to electrodes at
>>> both ends
>>> >> and will be mounted above a substrate, I assume the atoms in the
>>> >> structure are not completely free and thus I need to model them
>>> being
>>> >> restricted in their movement. Maybe position restraints are more
>>> >> appropriate than freezing to model such a situation.
>>> >>
>>> >> I do not see anything in the trajectory that provides clues as to
>>> what
>>> >> might be causing the segmentation fault.
>>> >>
>>> >
>>> >Then it will be very difficult to get any more remote help ;) If you
>>> >consistently get the crash between step 20,000 and 30,000, then
>>> perhaps split
>>> >your simulation into shorter sections, and during the time when you
>>> expect the
>>> >crash to occur, set nstxtcout = (some small value, like 1 or 10) to
>>> obtain the
>>> >most detail possible. At some point, something is going to go
>>> careening off
>>> >into infinity.
>>> >
>>> >-Justin
>>> >
>>> >> Thanks again for your help.
>>> >>
>>> >> Darrell
>>> >>
>>> >>> Date: Fri, 17 Jul 2009 19:08:38 -0400
>>> >>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> >>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>> >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >>> Message-ID: <4A610476.2090709 at vt.edu>
>>> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >>>
>>> >>>
>>> >>>
>>> >>> darrellk at ece.ubc.ca wrote:
>>> >>>> Hi Justin,
>>> >>>> I froze the graphene sheet because, prior to freezing it, I
>>> noticed that
>>> >>>> it was vibrating and thought that maybe its vibration was not
>>> allowing
>>> >>>> the NH3 molecules to adsorb (bond) to it. But after freezing the
>>> >>>> graphene sheet, I see that see that NH3 molecules are still not
>>> bonding
>>> >>>> to it. Physical experiments of NH3 and a graphene lattice
>>> connected to
>>> >>>> electrodes have shown that NH3 does adsorb to graphene, but all
>>> I see
>>> >>>> are NH3 molecules coming close to the graphene surface and then
>>> bouncing
>>> >>>> away which I am assuming is a result of repulsion between the
>>> negatively
>>> >>>> charged N atom in the ammonia molecule and the pi electrons in the
>>> >>>> graphene lattice. So I am not sure why experiments have shown
>>> adsorption
>>> >>>> unless adsoption is occurring as a result of a current flowing
>>> through
>>> >>>> the graphene structure or as a result of edge effects at the
>>> interface
>>> >>>> between the electrodes and the graphene lattice.
>>> >>>>
>>> >>> What parameters are you using for the species involved? Could be
>>> that there's
>>> >>> something wrong with your model.
>>> >>>
>>> >>>> Could you tell me how freezing is different that position
>>> restraining as
>>> >>>> this is not completely clear to me?
>>> >>>>
>>> >>> Freezing means positions are absolutely fixed and never updated.
>>> Position
>>> >>> restraining means there is an energy penalty to movement, but
>>> positions can
>>> >>> adjust slightly. I was thinking that if you have some strange
>>> interaction
>>> >>> happening, and freezing was preventing any reaction to the
>>> force, then you'd see
>>> >>> an explosion. I don't necessarily see why you need to apply
>>> either, but that
>>> >>> will depend on the extent of "vibration" that you see in the
>>> graphene sheet.
>>> >>> Are you applying improper dihedrals appropriately? Are the rings
>>> puckering, or
>>> >>> just vibrating slightly (which could be normal)?
>>> >>>
>>> >>>> I will try position restraining the graphene structure and see
>>> if that
>>> >>>> resolves my problem.
>>> >>>>
>>> >>>> I have been able to view a trajectory for simulations of fewer
>>> than
>>> >>>> 20,000 time steps and see the frozen graphene lattice and the NH3
>>> >>>> molecules floating through space.
>>> >>>>
>>> >>>> Note that the segmentation fault only occurs sometime between
>>> 20,000 and
>>> >>>> 30,000 time steps. Could it be that the "funky" behaviour
>>> associated
>>> >>>> with freezing would take 20,000+ time steps to cause a
>>> segmentation
>>> >>>> fault?
>>> >>>>
>>> >>> Depends entirely upon what's causing the explosion. Any clues
>>> from the trajectory?
>>> >>>
>>> >>> -Justin
>>> >>>
>>> >>>> Thanks again for your help.
>>> >>>>
>>> >>>> Darrell
>>> >>>>
>>> >>>>> Date: Thu, 16 Jul 2009 16:20:04 -0400
>>> >>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> >>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>>> >>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >>>>> Message-ID: <4A5F8B74.6070404 at vt.edu>
>>> >>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >>>>>
>>> >>>>>
>>> >>>>>
>>> >>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>> Hi Justin,
>>> >>>>>> Thanks for the explanation of the difference between EM &
>>> equilibration.
>>> >>>>>> Since in my model, I: (i) only have the graphene sheet and
>>> ammonia
>>> >>>>>> molecules spaced reasonably far apart from each other (1332 NH3
>>> >>>>>> molecules in a 38x38x38 box) and from the graphene sheet
>>> (distance
>>> >>>>>> between the closest ammonia molecule and the graphene sheet
>>> is greater
>>> >>>>>> than the molecular diameter of ammonia - maybe this is too
>>> close and
>>> >>>>>> could be causing my problem?); (ii) freeze the graphene
>>> sheet; I am
>>> >>>>>> thinking equilibration is not required in my model. Please
>>> let me know
>>> >>>>>> if you think I still need to perform equilibration.
>>> >>>>>>
>>> >>>>>> Yes, the EM did converge satisfactorily. Here is the output
>>> from EM:
>>> >>>>>> Steepest Descents converged to Fmax < 250 in 61 steps
>>> >>>>>> Potential Energy = 4.6094102e+04
>>> >>>>>> Maximum force = 2.4543298e+02 on atom 1
>>> >>>>>> Norm of force = 7.5803179e+03
>>> >>>>>>
>>> >>>>>> Is this a reasonable value for FMax?
>>> >>>>>>
>>> >>>>> Your Fmax looks fine. Why is it necessary to freeze the
>>> graphene sheet? Why
>>> >>>>> not use position restraints (to rule out funky behavior of
>>> being frozen)?
>>> >>>>>
>>> >>>>> Did you ever obtain a trajectory with enough frames that you
>>> could watch? What
>>> >>>>> happened?
>>> >>>>>
>>> >>>>> -Justin
>>> >>>>>
>>> >>>>>> Thanks again for your help.
>>> >>>>>>
>>> >>>>>> Darrell
>>> >>>>>>
>>> >>>>>>
>>> >>>>>>> Date: Thu, 16 Jul 2009 07:15:12 -0400
>>> >>>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> >>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not
>>> mapped)
>>> >>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >>>>>>> Message-ID: <4A5F0BC0.4020200 at vt.edu>
>>> >>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>>>> Hi Mark,
>>> >>>>>>>> I do not do any equilibration, I only do energy
>>> minimization as in the
>>> >>>>>>>> "GROMACS Tutorial for Solvation Study of Spider Toxin
>>> Peptide". Please
>>> >>>>>>>> let me know if I need to do equilibration and what is the
>>> difference
>>> >>>>>>>> between energy minimization and equilibration as this is
>>> not clear to me.
>>> >>>>>>>>
>>> >>>>>>> Did the EM converge satisfactorily? What was Fmax?
>>> >>>>>>>
>>> >>>>>>> Unlike EM, equilibration is an MD process; for a protein
>>> system, one generally
>>> >>>>>>> position-restrains the protein and allows the surrounding
>>> solvent to optimize
>>> >>>>>>> around the structure.
>>> >>>>>>>
>>> >>>>>>> -Justin
>>> >>>>>>>
>>> >>>>>>>> Here is an mdp file for a run that actually completed
>>> successfully:
>>> >>>>>>>> title =Graphene
>>> >>>>>>>> ;warnings =10
>>> >>>>>>>> cpp =cpp
>>> >>>>>>>> ;define =-DPOSRES
>>> >>>>>>>> constraints =none
>>> >>>>>>>> integrator =md
>>> >>>>>>>> dt =0.002 ; ps
>>> >>>>>>>> nsteps =10000
>>> >>>>>>>> nstcomm =100
>>> >>>>>>>> nstxout =100
>>> >>>>>>>> ;nstvout =1000
>>> >>>>>>>> nstfout =0
>>> >>>>>>>> nstlog =100
>>> >>>>>>>> nstenergy =100
>>> >>>>>>>> nstlist =100
>>> >>>>>>>> ns_type =grid
>>> >>>>>>>> rlist =2.0
>>> >>>>>>>> coulombtype =PME
>>> >>>>>>>> rcoulomb =2.0
>>> >>>>>>>> vdwtype =cut-off
>>> >>>>>>>> rvdw =5.0
>>> >>>>>>>> fourierspacing =0.12
>>> >>>>>>>> fourier_nx =0
>>> >>>>>>>> fourier_ny =0
>>> >>>>>>>> fourier_nz =0
>>> >>>>>>>> pme_order =4
>>> >>>>>>>> ewald_rtol =1e-5
>>> >>>>>>>> optimize_fft =yes
>>> >>>>>>>>
>>> >>>>>>>> ; This section freezes graphene lattice
>>> >>>>>>>> energygrps = Grph NH3
>>> >>>>>>>> energygrp_excl = Grph Grph
>>> >>>>>>>> freezegrps = Grph ; Freeze graphene lattice
>>> >>>>>>>> freezedim = Y Y Y; in all directions
>>> >>>>>>>>
>>> >>>>>>>> Tcoupl =berendsen
>>> >>>>>>>> tau_t =0.5 0.5
>>> >>>>>>>> tc-grps =NH3 Grph
>>> >>>>>>>> ref_t =300 300
>>> >>>>>>>>
>>> >>>>>>>> ;coupl = parrinello-rahman
>>> >>>>>>>> ;tau_p = 1.5
>>> >>>>>>>> ;compressibility = 1.3
>>> >>>>>>>> ;ref_p = 0.061
>>> >>>>>>>>
>>> >>>>>>>> gen_vel = yes
>>> >>>>>>>> gen_temp = 300.0
>>> >>>>>>>> gen_seed = 173529
>>> >>>>>>>>
>>> >>>>>>>> And here is a copy of an mdp file for a run that did not
>>> complete
>>> >>>>>>>> successfully:
>>> >>>>>>>>
>>> >>>>>>>> title =Graphene
>>> >>>>>>>> ;warnings =10
>>> >>>>>>>> cpp =cpp
>>> >>>>>>>> ;define =-DPOSRES
>>> >>>>>>>> constraints =none
>>> >>>>>>>> integrator =md
>>> >>>>>>>> dt =0.002 ; ps
>>> >>>>>>>> nsteps =30000
>>> >>>>>>>> nstcomm =500
>>> >>>>>>>> nstxout =500
>>> >>>>>>>> ;nstvout =1000
>>> >>>>>>>> nstfout =0
>>> >>>>>>>> nstlog =500
>>> >>>>>>>> nstenergy =500
>>> >>>>>>>> nstlist =500
>>> >>>>>>>> ns_type =grid
>>> >>>>>>>> rlist =2.0
>>> >>>>>>>> coulombtype =PME
>>> >>>>>>>> rcoulomb =2.0
>>> >>>>>>>> vdwtype =cut-off
>>> >>>>>>>> rvdw =5.0
>>> >>>>>>>> fourierspacing =0.12
>>> >>>>>>>> fourier_nx =0
>>> >>>>>>>> fourier_ny =0
>>> >>>>>>>> fourier_nz =0
>>> >>>>>>>> pme_order =4
>>> >>>>>>>> ewald_rtol =1e-5
>>> >>>>>>>> optimize_fft =yes
>>> >>>>>>>>
>>> >>>>>>>> ; This section freezes graphene lattice
>>> >>>>>>>> energygrps = Grph NH3
>>> >>>>>>>> energygrp_excl = Grph Grph
>>> >>>>>>>> freezegrps = Grph ; Freeze graphene lattice
>>> >>>>>>>> freezedim = Y Y Y; in all directions
>>> >>>>>>>>
>>> >>>>>>>> Tcoupl =berendsen
>>> >>>>>>>> tau_t =0.5 0.5
>>> >>>>>>>> tc-grps =NH3 Grph
>>> >>>>>>>> ref_t =300 300
>>> >>>>>>>>
>>> >>>>>>>> ;coupl = parrinello-rahman
>>> >>>>>>>> ;tau_p = 1.5
>>> >>>>>>>> ;compressibility = 1.3
>>> >>>>>>>> ;ref_p = 0.061
>>> >>>>>>>>
>>> >>>>>>>> gen_vel = yes
>>> >>>>>>>> gen_temp = 300.0
>>> >>>>>>>> gen_seed = 173529
>>> >>>>>>>>
>>> >>>>>>>> Please let me know what you think might be the problem.
>>> >>>>>>>>
>>> >>>>>>>> Thanks
>>> >>>>>>>>
>>> >>>>>>>> Darrell
>>> >>>>>>>>
>>> >>>>>>>>> Date: Thu, 16 Jul 2009 09:47:49 +1000
>>> >>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> >>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not
>>> mapped)
>>> >>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>> >>>>>>>>> Message-ID: <4A5E6AA5.4040809 at anu.edu.au>
>>> >>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >>>>>>>>>
>>> >>>>>>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>>>>>> Hi Mark,
>>> >>>>>>>>>> Yes, I know that the box dimensions are defined in the
>>> last line of the
>>> >>>>>>>>>> .gro file and I have defined these dimensions as 38 nm x
>>> 38 nm x 38 nm
>>> >>>>>>>>>> in the .gro file.
>>> >>>>>>>>> OK.
>>> >>>>>>>>>
>>> >>>>>>>>>> I looked through my .gro file to ensure none of the atoms
>>> had coordinates
>>> >>>>>>>>>> outside the 38x38x38 box. While I was reviewing the file
>>> I did notice
>>> >>>>>>>>>> that some coordinates had negative values, slightly
>>> negative, but
>>> >>>>>>>>>> negative none the less. Could this be causing the
>>> segmentation fault
>>> >>>>>>>>>> between time step 10,000 and time step 30,000? Why
>>> wouldn't the
>>> >>>>>>>>>> negative coordinates cause a segmentation fault much
>>> earlier?
>>> >>>>>>>>> The absolute value of the coordinates is irrelevant.
>>> >>>>>>>>>
>>> >>>>>>>>> Your choice of 2.0 for rcoulomb is likely suboptimal for
>>> PME. Some
>>> >>>>>>>>> smaller value is probably more efficient, but this will
>>> not be the cause
>>> >>>>>>>>> of your problem.
>>> >>>>>>>>>
>>> >>>>>>>>> What is your system preparation regime? (i.e. EM +
>>> equilibration)
>>> >>>>>>>>>
>>> >>>>>>>>> Can you post a corrected and current .mdp file?
>>> >>>>>>>>>
>>> >>>>>>>>> Mark
>>> >>>>>>>>>
>>> >>>>>>>>>>> Date: Wed, 15 Jul 2009 16:59:21 +1000
>>> >>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> >>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not
>>> mapped)
>>> >>>>>>>>>>> To: Discussion list for GROMACS users
>>> <gmx-users at gromacs.org>
>>> >>>>>>>>>>> Message-ID: <4A5D7E49.9020700 at anu.edu.au>
>>> >>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>>>>>>>> Hi Justin,
>>> >>>>>>>>>>>> I was experiencing the problem before someone suggested
>>> using editconf so
>>> >>>>>>>>>>>> I do not think the problem is being caused by editconf.
>>> But anyway here
>>> >>>>>>>>>>>> is my editconf command. Let me know if you a source of
>>> error in this
>>> >>>>>>>>>>>> command line.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> editconf -f graphene.gro -n index.ndx -o graphene_ec.gro
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> I did not want to add in additional space between the
>>> solvent and the box
>>> >>>>>>>>>>>> as I saw no reason for doing so. And hence that is why
>>> I originally did
>>> >>>>>>>>>>>> not use editconf.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> My box dimensions are 38nm x 38nm x 38nm.
>>> >>>>>>>>>>> The box dimensions are defined in the bottom line of the
>>> .gro file, and
>>> >>>>>>>>>>> not by the positions of the atoms in that file. If you
>>> haven't ever set
>>> >>>>>>>>>>> them to be suitable for your coordinates with editconf,
>>> then they might
>>> >>>>>>>>>>> not be.
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> Mark
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> I used cutoffs of 2 nm & 5 nm
>>> >>>>>>>>>>>> for my system so ensure the cutoff occured at a
>>> distance where the
>>> >>>>>>>>>>>> potentials were stabalized (not changing). I guess I
>>> could use shorter
>>> >>>>>>>>>>>> cutoffs such as 1.5 nm & 2 nm and this may decrease my
>>> computation time.
>>> >>>>>>>>>>>> I also thought that I needed to use larger cut-offs
>>> since I am dealing
>>> >>>>>>>>>>>> in the gas phase and there is greater ditance between
>>> the atoms in my
>>> >>>>>>>>>>>> simulation than in liquid-based simulations.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> In the .log files, I do not see any LINCS warnings or
>>> neighborlist
>>> >>>>>>>>>>>> errors.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> I ran gmxcheck on a .trr file and was presented with
>>> the following
>>> >>>>>>>>>>>> output:
>>> >>>>>>>>>>>> *********************************************
>>> >>>>>>>>>>>> Checking file mdtraj.trr
>>> >>>>>>>>>>>> trn version: GMX_trn_file (single precision)
>>> >>>>>>>>>>>> Reading frame 0 time 0.000
>>> >>>>>>>>>>>> # Atoms 10482
>>> >>>>>>>>>>>> Last frame 5 time 1.000
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> Item #frames Timestep (ps)
>>> >>>>>>>>>>>> Step 6 0.2
>>> >>>>>>>>>>>> Time 6 0.2
>>> >>>>>>>>>>>> Lambda 6 0.2
>>> >>>>>>>>>>>> Coords 6 0.2
>>> >>>>>>>>>>>> Velocities 6 0.2
>>> >>>>>>>>>>>> Forces 0
>>> >>>>>>>>>>>> Box 6 0.2
>>> >>>>>>>>>>>> *********************************************
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> I ran two additional simulations with different values
>>> for nsteps and
>>> >>>>>>>>>>>> nstxxxx paramaters and have the following to report:
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> When I run a simulation with the following parameters
>>> it completes
>>> >>>>>>>>>>>> successfully and I see, in the log file, the system
>>> output every 100
>>> >>>>>>>>>>>> time steps.
>>> >>>>>>>>>>>> nsteps =10000
>>> >>>>>>>>>>>> nstcomm =100
>>> >>>>>>>>>>>> nstxout =100
>>> >>>>>>>>>>>> nstfout =0
>>> >>>>>>>>>>>> nstlog =100
>>> >>>>>>>>>>>> nstenergy =100
>>> >>>>>>>>>>>> nstlist =100
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> When I run a simulation with the following parameters
>>> it fails with a
>>> >>>>>>>>>>>> sementation fault and, in the log file, I do not see
>>> system output every
>>> >>>>>>>>>>>> 500 time steps.
>>> >>>>>>>>>>>> nsteps =30000
>>> >>>>>>>>>>>> nstcomm =500
>>> >>>>>>>>>>>> nstxout =500
>>> >>>>>>>>>>>> nstfout =0
>>> >>>>>>>>>>>> nstlog =500
>>> >>>>>>>>>>>> nstenergy =500
>>> >>>>>>>>>>>> nstlist =500
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> Please let me know what you think might be the problem.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> Thank you very much.
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>> Darrell
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>>>> Date: Mon, 13 Jul 2009 15:37:15 -0400
>>> >>>>>>>>>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>>> >>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address
>>> not mapped)
>>> >>>>>>>>>>>>> To: Discussion list for GROMACS users
>>> <gmx-users at gromacs.org>
>>> >>>>>>>>>>>>> Message-ID: <4A5B8CEB.4020609 at vt.edu>
>>> >>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>>> format=flowed
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>>>>>>>>>> Hi Mark,
>>> >>>>>>>>>>>>>> I used editconf on my .gro file with zero space
>>> between my solvent and
>>> >>>>>>>>>>>>>> the box and the resulting box had the exact same
>>> dimension as the
>>> >>>>>>>>>>>>>> initial box. I also performed a number of simulation
>>> runs with different
>>> >>>>>>>>>>>>> If you're using editconf to define zero space, what's
>>> the point? I only ask
>>> >>>>>>>>>>>>> because it is a potential source of error if you think
>>> you're adding zero space,
>>> >>>>>>>>>>>>> but something else might be going on. Maybe you can
>>> post your editconf command
>>> >>>>>>>>>>>>> line.
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> What are your box dimensions? Are cut-off lengths of
>>> 2.0 and 5.0 nm appropriate
>>> >>>>>>>>>>>>> for your system? How did you determine that these
>>> cut-off's should be used?
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>> mdp parameters hoping this would provide me some
>>> indication of the cause
>>> >>>>>>>>>>>>>> of the fault but to no avail. I looked through the
>>> log files, error
>>> >>>>>>>>>>>>>> files, and output files and could not find any output
>>> to help me
>>> >>>>>>>>>>>>>> identify the source of my error.
>>> >>>>>>>>>>>>>>
>>> >>>>>>>>>>>>> It is very odd that Gromacs isn't report anything at
>>> all. No LINCS warnings?
>>> >>>>>>>>>>>>> No neighborlist errors? These would be in the .log file.
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>> Could you please let me know how I can look at my
>>> structure at each point
>>> >>>>>>>>>>>>>> as you indicate below as I do not see any files
>>> output that provide me
>>> >>>>>>>>>>>>>> to do so? I tried to look at the .trr file but when I
>>> try to load it
>>> >>>>>>>>>>>>>> into VMD, it causes an error. I am assuming this
>>> error is caused because
>>> >>>>>>>>>>>>>> the .trr file did not complete correctly due to the
>>> segmentation fault.
>>> >>>>>>>>>>>>>> Please advise.
>>> >>>>>>>>>>>>>>
>>> >>>>>>>>>>>>> How early is the segmentation fault occurring? I have
>>> found it useful sometimes
>>> >>>>>>>>>>>>> to set nstxout (or nstxtcout) = 1 to try to catch the
>>> first few frames if the
>>> >>>>>>>>>>>>> explosion is occurring early. In any case, gmxcheck
>>> will help determine how
>>> >>>>>>>>>>>>> many frames are present, as well as the integrity of
>>> the file (broken frames, etc).
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> -Justin
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>>> Thanks.
>>> >>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>> Darrell
>>> >>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>> Date: Tue, 07 Jul 2009 09:19:42 +1000
>>> >>>>>>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> >>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address
>>> not mapped)
>>> >>>>>>>>>>>>>>> To: Discussion list for GROMACS users
>>> <gmx-users at gromacs.org>
>>> >>>>>>>>>>>>>>> Message-ID: <4A52868E.6010807 at anu.edu.au>
>>> >>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>>> format=flowed
>>> >>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>>>>>>>>>>>> Hi Mark,
>>> >>>>>>>>>>>>>>>> I added the energy group exclusions as indicated in
>>> your previous
>>> >>>>>>>>>>>>>>>> response but am still experiencing the same
>>> problem. I looked at the
>>> >>>>>>>>>>>>>>>> .log files and see that in one log file it tells me
>>> that my box is
>>> >>>>>>>>>>>>>>>> exploding. However, I do not have many molecules in
>>> my simulation and
>>> >>>>>>>>>>>>>>>> therefore do not think that it is possible that my
>>> box is exploding from
>>> >>>>>>>>>>>>>>>> pressure.
>>> >>>>>>>>>>>>>>> Sure, but if there's something malformed with your
>>> model physics or
>>> >>>>>>>>>>>>>>> starting configuration, then large forces can make
>>> anything explode.
>>> >>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>> Look at your structures at each point and see where
>>> things start to go
>>> >>>>>>>>>>>>>>> wrong. Make sure you've used editconf on your
>>> starting structure to
>>> >>>>>>>>>>>>>>> provide the right box dimensions.
>>> >>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>> Mark
>>> >>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>> Maybe if I re-state my simulation it will help you
>>> in providing me
>>> >>>>>>>>>>>>>>>> direction on what might be causing the problem. My
>>> simulation consists
>>> >>>>>>>>>>>>>>>> of a graphene lattice with a layer of ammonia
>>> molecules above it. The
>>> >>>>>>>>>>>>>>>> box is very large and there is lots of empty space
>>> in the box. So I am a
>>> >>>>>>>>>>>>>>>> little confused as to how the box could be exploding.
>>> >>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>> Thanks again in advance for your help.
>>> >>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>> Darrell Koskinen
>>> >>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>> Date: Fri, 03 Jul 2009 11:41:45 +1000
>>> >>>>>>>>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>>> >>>>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault
>>> (Address not mapped)
>>> >>>>>>>>>>>>>>>>> To: Discussion list for GROMACS users
>>> <gmx-users at gromacs.org>
>>> >>>>>>>>>>>>>>>>> Message-ID: <4A4D61D9.6080700 at anu.edu.au>
>>> >>>>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>>> format=flowed
>>> >>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>>> >>>>>>>>>>>>>>>>>> Dear GROMACS Gurus,
>>> >>>>>>>>>>>>>>>>>> I am experiencing a segmentation fault when mdrun
>>> executes. My simulation
>>> >>>>>>>>>>>>>>>>>> has a graphene lattice with an array (layer) of
>>> ammonia molecules above
>>> >>>>>>>>>>>>>>>>>> it. The box is three times the width of the
>>> graphene lattice, three
>>> >>>>>>>>>>>>>>>>>> times the length of the graphene lattice, and
>>> three times the height
>>> >>>>>>>>>>>>>>>>>> between the graphene lattice and the ammonia
>>> molecules. I am including
>>> >>>>>>>>>>>>>>>>>> the mdp file and the error message.
>>> >>>>>>>>>>>>>>>>> Probably your system is exploding when integration
>>> fails with excessive
>>> >>>>>>>>>>>>>>>>> forces. You should look at the bottom of stdout,
>>> stderr, *and* the .log
>>> >>>>>>>>>>>>>>>>> file to diagnose. The error message you give below
>>> is merely the
>>> >>>>>>>>>>>>>>>>> diagnostic trace from the MPI library, and it not
>>> useful for finding out
>>> >>>>>>>>>>>>>>>>> what GROMACS thinks the problem might be. Further
>>> advice below.
>>> >>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>>
>>> ***************************************************************************
>>>
>>> >>>>>>>>>>>>>>>>>> .mdp file
>>> >>>>>>>>>>>>>>>>>> title =FWS
>>> >>>>>>>>>>>>>>>>>> ;warnings =10
>>> >>>>>>>>>>>>>>>>>> cpp =cpp
>>> >>>>>>>>>>>>>>>>>> ;define =-DPOSRES
>>> >>>>>>>>>>>>>>>>>> ;constraints =all-bonds
>>> >>>>>>>>>>>>>>>>>> integrator =md
>>> >>>>>>>>>>>>>>>>>> dt =0.002 ; ps
>>> >>>>>>>>>>>>>>>>>> nsteps =100000
>>> >>>>>>>>>>>>>>>>>> nstcomm =1000
>>> >>>>>>>>>>>>>>>>>> nstxout =1000
>>> >>>>>>>>>>>>>>>>>> ;nstvout =1000
>>> >>>>>>>>>>>>>>>>>> nstfout =0
>>> >>>>>>>>>>>>>>>>>> nstlog =1000
>>> >>>>>>>>>>>>>>>>>> nstenergy =1000
>>> >>>>>>>>>>>>>>>>>> nstlist =1000
>>> >>>>>>>>>>>>>>>>>> ns_type =grid
>>> >>>>>>>>>>>>>>>>>> rlist =2.0
>>> >>>>>>>>>>>>>>>>>> coulombtype =PME
>>> >>>>>>>>>>>>>>>>>> rcoulomb =2.0
>>> >>>>>>>>>>>>>>>>>> vdwtype =cut-off
>>> >>>>>>>>>>>>>>>>>> rvdw =5.0
>>> >>>>>>>>>>>>>>>>>> fourierspacing =0.12
>>> >>>>>>>>>>>>>>>>>> fourier_nx =0
>>> >>>>>>>>>>>>>>>>>> fourier_ny =0
>>> >>>>>>>>>>>>>>>>>> fourier_nz =0
>>> >>>>>>>>>>>>>>>>>> pme_order =4
>>> >>>>>>>>>>>>>>>>>> ewald_rtol =1e-5
>>> >>>>>>>>>>>>>>>>>> optimize_fft =yes
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> ; This section added in to freeze hydrogen atoms
>>> at edge of graphene
>>> >>>>>>>>>>>>>>>>>> lattice to prevent movement of lattice
>>> >>>>>>>>>>>>>>>>>> ;energygrp_excl = Edge Edge Edge Grph Grph Grph
>>> >>>>>>>>>>>>>>>>>> freezegrps = Edge Grph ; Hydrogen atoms in
>>> graphene lattice are
>>> >>>>>>>>>>>>>>>>>> associated with the residue Edge
>>> >>>>>>>>>>>>>>>>> See comments in 7.3.24 of manual. You need the
>>> energy group exclusions.
>>> >>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>> Mark
>>> >>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in
>>> all directions
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> ;Tcoupl =berendsen
>>> >>>>>>>>>>>>>>>>>> ;tau_t =0.1 0.1
>>> >>>>>>>>>>>>>>>>>> ;tc-grps =protein non-protein
>>> >>>>>>>>>>>>>>>>>> ;ref_t = 300 300
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> ;Pcoupl = parrinello-rahman
>>> >>>>>>>>>>>>>>>>>> ;tau_p = 0.5
>>> >>>>>>>>>>>>>>>>>> ;compressibility = 4.5e-5
>>> >>>>>>>>>>>>>>>>>> ;ref_p = 1.0
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> ;gen_vel = yes
>>> >>>>>>>>>>>>>>>>>> ;gen_temp = 300.0
>>> >>>>>>>>>>>>>>>>>> ;gen_seed = 173529
>>> >>>>>>>>>>>>>>>>>>
>>> ***************************************************************************
>>>
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>>
>>> ***************************************************************************
>>>
>>> >>>>>>>>>>>>>>>>>> ERROR IN OUTPUT FILE
>>> >>>>>>>>>>>>>>>>>> [node16:25758] *** Process received signal ***
>>> >>>>>>>>>>>>>>>>>> [node16:25758] Signal: Segmentation fault (11)
>>> >>>>>>>>>>>>>>>>>> [node16:25758] Signal code: Address not mapped (1)
>>> >>>>>>>>>>>>>>>>>> [node16:25758] Failing at address:
>>> 0xfffffffe1233e230
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 0] /lib64/libpthread.so.0
>>> [0x3834a0de80]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 1]
>>> /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6)
>>> >>>>>>>>>>>>>>>>>> [0x2ba295dd0606]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 2]
>>> /usr/lib64/libmd_mpi.so.4(do_pme+0x808)
>>> >>>>>>>>>>>>>>>>>> [0x2ba295dd4058]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 3]
>>> /usr/lib64/libmd_mpi.so.4(force+0x8de)
>>> >>>>>>>>>>>>>>>>>> [0x2ba295dba5be]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 4]
>>> /usr/lib64/libmd_mpi.so.4(do_force+0x5ef)
>>> >>>>>>>>>>>>>>>>>> [0x2ba295ddeaff]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 5] mdrun_mpi(do_md+0xe23)
>>> [0x411193]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40)
>>> [0x4142f0]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 8]
>>> /lib64/libc.so.6(__libc_start_main+0xf4)
>>> >>>>>>>>>>>>>>>>>> [0x3833e1d8b4]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 9] mdrun_mpi [0x40429a]
>>> >>>>>>>>>>>>>>>>>> [node16:25758] *** End of error message ***
>>> >>>>>>>>>>>>>>>>>> mpirun noticed that job rank 7 with PID 25758 on
>>> node node16 exited on
>>> >>>>>>>>>>>>>>>>>> signal 11 (Segmentation fault).
>>> >>>>>>>>>>>>>>>>>> 7 processes killed (possibly by Open MPI)
>>> >>>>>>>>>>>>>>>>>>
>>> ***************************************************************************
>>>
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> Could you please let me know what you think may
>>> be causing the fault?
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> Much thanks in advance.
>>> >>>>>>>>>>>>>>>>>>
>>> >>>>>>>>>>>>>>>>>> Darrell Koskinen
>>> >>>>>>>>>>>>>> _______________________________________________
>>> >>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>> >>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>>>>>>>>>> Please search the archive at
>>> http://www.gromacs.org/search before posting!
>>> >>>>>>>>>>>>>> Please don't post (un)subscribe requests to the list.
>>> Use the
>>> >>>>>>>>>>>>>> www interface or send it to
>>> gmx-users-request at gromacs.org.
>>> >>>>>>>>>>>>>> Can't post? Read
>>> http://www.gromacs.org/mailing_lists/users.php
>>> >>>>>>>>>>>>>>
>>> >>>>>>>>>>>>> --
>>> >>>>>>>>>>>>> ========================================
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> Justin A. Lemkul
>>> >>>>>>>>>>>>> Ph.D. Candidate
>>> >>>>>>>>>>>>> ICTAS Doctoral Scholar
>>> >>>>>>>>>>>>> Department of Biochemistry
>>> >>>>>>>>>>>>> Virginia Tech
>>> >>>>>>>>>>>>> Blacksburg, VA
>>> >>>>>>>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>> >>>>>>>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> >>>>>>>>>>>>>
>>> >>>>>>>>>>>>> ========================================
>>> >>>>>>>>>>>> _______________________________________________
>>> >>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>> >>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>>>>>>>> Please search the archive at
>>> http://www.gromacs.org/search before posting!
>>> >>>>>>>>>>>> Please don't post (un)subscribe requests to the list.
>>> Use the
>>> >>>>>>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>> >>>>>>>>>>>> Can't post? Read
>>> http://www.gromacs.org/mailing_lists/users.php
>>> >>>>>>>>>>>>
>>> >>>>>>>>>>> ------------------------------
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> _______________________________________________
>>> >>>>>>>>>>> gmx-users mailing list
>>> >>>>>>>>>>> gmx-users at gromacs.org
>>> >>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>>>>>>> Please search the archive at
>>> http://www.gromacs.org/search before posting!
>>> >>>>>>>>>>>
>>> >>>>>>>>>>> End of gmx-users Digest, Vol 63, Issue 61
>>> >>>>>>>>>>> *****************************************
>>> >>>>>>>>>>>
>>> >>>>>>>>>> _______________________________________________
>>> >>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>> >>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>>>>>> Please search the archive at
>>> http://www.gromacs.org/search before posting!
>>> >>>>>>>>>> Please don't post (un)subscribe requests to the list. Use
>>> the
>>> >>>>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>> >>>>>>>>>> Can't post? Read
>>> http://www.gromacs.org/mailing_lists/users.php
>>> >>>>>>>>>>
>>> >>>>>>>> _______________________________________________
>>> >>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>> >>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>>>> Please search the archive at http://www.gromacs.org/search
>>> before posting!
>>> >>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>>> >>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>> >>>>>>>> Can't post? Read
>>> http://www.gromacs.org/mailing_lists/users.php
>>> >>>>>>>>
>>> >>>>>>> --
>>> >>>>>>> ========================================
>>> >>>>>>>
>>> >>>>>>> Justin A. Lemkul
>>> >>>>>>> Ph.D. Candidate
>>> >>>>>>> ICTAS Doctoral Scholar
>>> >>>>>>> Department of Biochemistry
>>> >>>>>>> Virginia Tech
>>> >>>>>>> Blacksburg, VA
>>> >>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>>> >>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> >>>>>>>
>>> >>>>>>> ========================================
>>> >>>>>>>
>>> >>>>>>>
>>> >>>>>>> ------------------------------
>>> >>>>>>>
>>> >>>>>>> _______________________________________________
>>> >>>>>>> gmx-users mailing list
>>> >>>>>>> gmx-users at gromacs.org
>>> >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>>> Please search the archive at http://www.gromacs.org/search
>>> before posting!
>>> >>>>>>>
>>> >>>>>>> End of gmx-users Digest, Vol 63, Issue 74
>>> >>>>>>> *****************************************
>>> >>>>>>>
>>> >>>>>> _______________________________________________
>>> >>>>>> gmx-users mailing list gmx-users at gromacs.org
>>> >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>>> Please search the archive at http://www.gromacs.org/search
>>> before posting!
>>> >>>>>> Please don't post (un)subscribe requests to the list. Use the
>>> >>>>>> www interface or send it to gmx-users-request at gromacs.org.
>>> >>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>> >>>>>>
>>> >>>>> --
>>> >>>>> ========================================
>>> >>>>>
>>> >>>>> Justin A. Lemkul
>>> >>>>> Ph.D. Candidate
>>> >>>>> ICTAS Doctoral Scholar
>>> >>>>> Department of Biochemistry
>>> >>>>> Virginia Tech
>>> >>>>> Blacksburg, VA
>>> >>>>> jalemkul[at]vt.edu | (540) 231-9080
>>> >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> >>>>>
>>> >>>>> ========================================
>>> >>>>>
>>> >>>>>
>>> >>>>> ------------------------------
>>> >>>>>
>>> >>>>> _______________________________________________
>>> >>>>> gmx-users mailing list
>>> >>>>> gmx-users at gromacs.org
>>> >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>>> Please search the archive at http://www.gromacs.org/search
>>> before posting!
>>> >>>>>
>>> >>>>> End of gmx-users Digest, Vol 63, Issue 79
>>> >>>>> *****************************************
>>> >>>>>
>>> >>>> _______________________________________________
>>> >>>> gmx-users mailing list gmx-users at gromacs.org
>>> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>>> Please search the archive at http://www.gromacs.org/search
>>> before posting!
>>> >>>> Please don't post (un)subscribe requests to the list. Use the
>>> >>>> www interface or send it to gmx-users-request at gromacs.org.
>>> >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>> >>>>
>>> >>> --
>>> >>> ========================================
>>> >>>
>>> >>> Justin A. Lemkul
>>> >>> Ph.D. Candidate
>>> >>> ICTAS Doctoral Scholar
>>> >>> Department of Biochemistry
>>> >>> Virginia Tech
>>> >>> Blacksburg, VA
>>> >>> jalemkul[at]vt.edu | (540) 231-9080
>>> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> >>>
>>> >>> ========================================
>>> >>>
>>> >>>
>>> >>> ------------------------------
>>> >>>
>>> >>> _______________________________________________
>>> >>> gmx-users mailing list
>>> >>> gmx-users at gromacs.org
>>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >>> Please search the archive at http://www.gromacs.org/search
>>> before posting!
>>> >>>
>>> >>> End of gmx-users Digest, Vol 63, Issue 85
>>> >>> *****************************************
>>> >>>
>>> >> _______________________________________________
>>> >> gmx-users mailing list gmx-users at gromacs.org
>>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> >> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> >> Please don't post (un)subscribe requests to the list. Use the
>>> >> www interface or send it to gmx-users-request at gromacs.org.
>>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>> >>
>>> >
>>> >--
>>> >========================================
>>> >
>>> >Justin A. Lemkul
>>> >Ph.D. Candidate
>>> >ICTAS Doctoral Scholar
>>> >Department of Biochemistry
>>> >Virginia Tech
>>> >Blacksburg, VA
>>> >jalemkul[at]vt.edu | (540) 231-9080
>>> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>>
>>
>>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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