[gmx-users] Segmentation Fault (Address not mapped)

Darrell Koskinen darrellk at ece.ubc.ca
Mon Jul 27 23:33:05 CEST 2009


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?

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.

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?

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"

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?

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 
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 >>>>>>>>>> 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 
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 >>>>>>>> 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!
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 >>>> 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



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