[gmx-users] Segmentation Fault (Address not mapped)
darrellk at ece.ubc.ca
darrellk at ece.ubc.ca
Sat Jul 18 03:53:18 CEST 2009
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?
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.
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.
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
>*****************************************
>
More information about the gromacs.org_gmx-users
mailing list