[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
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>>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> ========================================
>>>>>>>>>>>>>
>>>>>>>>>>>>> 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
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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
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
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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!
>>>> 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
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