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

[Justin A. Lemkul]

Darrell Koskinen wrote:
> Hi Justin,
> With regard to your comment about using other force fields for my 
> simulation of graphene surrounded by ammonia gas, are referring to the 
> force fields for both graphene and ammonia or only to the force field 
> for graphene?
> 

The "force field" should be one in the same.  The parameters should be suitably 
derived using the same scheme as the original work.

> I reviewed my selection of the force field parameters for graphene and 
> see that I selected the parameters from the paper by Cornell et al. 
> since a paper on deformation of carbon nanotubes ("A structural 
> mechanics approach for the analysis of carbon nanotubes" by Chunyu Li, 
> Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003) 
> 2487–2499) used parameters from the paper by Cornell et al. Is this 
> sufficient to justify the use of these parameters? I also thought that 
> graphene and ammonia would be considered organic since they are 
> comprised of carbon, nitrogen, and hydrogen, which are all common 
> elements found in organic matter.
> 

If you feel that precedent is sufficient, then I guess go ahead.  But realize 
that the paper by Cornell et al. refers to parameters suitable for simulations 
of proteins and nucleic acids, as well as a few organic functional groups. 
Parameterization was based on peptide backbone geometry, as well as other 
parameters, likely none of which involved graphene and gaseous ammonia (they 
were doing liquid simulations).

> With regard to the parameters for ammonia, is it acceptable to use the 
> parameters from the paper by Cornell et al. or do I need to find papers 
> specifically related to ammonia gas molecular dynamics simulations?
> 

I would seriously consider finding parameters (if they exist) that have been 
derived for use with gas-phase simulations.

> With regard to dihedral selection, I looked at the .top file and see 
> that the function type is listed as 3 in the dihedrals section, which I 
> believe indicates that my simulation is using a Ryckaert-Bellemans 
> function. It appears to me that if I am using the OPLS force field that 
> the Ryckaert-Bellemans dihedral type is automatically selected. I do see 
> in the ffoplsaabon.itp file that there is an improper dihedral 
> definition which think I could potentially use in my simulation 
> "improper_Z_CA_X_Y", but how do I cause my simulation to use this 
> definition? Do I need to add the following line to my .top file?
> "#define improper_Z_CA_X_Y"
> 

No, you would have to use a special dihedrals section, that specifies the four 
atoms involved (function type 1), followed by the specification of that 
particular improper ("improper_Z_CA_X_Y").  See the manual for more details, 
and/or generate a topology for a protein with pdb2gmx with OPLS-AA and see how 
they're defined.

> Further, I thought that I could simply modify the appropriate lines of 
> the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found 
> in the paper by Cornell et al. so that they will be used in my 
> simulation. Am I correct in my assumption?
> 

Modifying ffoplsaa files to parameters that are not OPLS-AA is probably a bad 
choice.  If you're dead-set on using these parameters, download the ffamber 
ports and use the ffamber94 force field, not some Frankensteined-OPLS.  Besides, 
all of the parameters in the Cornell paper are in kcal/mol/A^2, which will 
require conversion to Gromacs standard units.  If you've printed them directly 
in your previous attempts, I can guarantee you you're not getting the values you 
think you are.

-Justin

> Thanks again for your help.
> 
> Darrell
> 
> 
>  >Date: Fri, 17 Jul 2009 22:11:07 -0400
>  >From: "Justin A. Lemkul" <jalemkul at vt.edu>
>  >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>  >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >Message-ID: <4A612F3B.7060503 at vt.edu>
>  >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >
>  >
>  >
>  >darrellk at ece.ubc.ca wrote:
>  >> Hi Justin,
>  >> I am using the ffoplsaabon.itp parameters for:
>  >> bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3)
>  >> angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H)
>  >> dihedrals (X-CA-CA-X, X-CA-CT-X)
>  >>
>  >> I am using the ffolpsaanb.itp VdW parameters for H & N3
>  >>
>  >> And I am using the VdW parameters found in the paper "A Second
>  >> Generation Force Field for the Simulation of Proteins, Nucleic Acids,
>  >> and Organic Molecules" for CA, HA, CT, & HC doing the conversion from
>  >> Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from
>  >> kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon. 
> The
>  >> converted parameters for sigma were different by only +/-2% to +/-8%
>  >> from the values in ffoplsaanb.itp, but the converted parameters for
>  >> epsilon were different by +/-23% to +/-66% from the values in
>  >> ffoplsaanb.itp. Is this a valid paper to use for selection of 
> parameters?
>  >>
>  >
>  >If memory serves, that paper is the derivation by Cornell, et al. for the
>  >AMBER94 parameter set, so no, you are not going to find those same 
> parameters in
>  >ffoplsaanb.itp.
>  >
>  >Furthermore, the title of the paper indicates that the parameters are for
>  >proteins, nucleic acids, and organic molecules. Has anyone else in the
>  >literature used these parameters for graphene lattices? I would 
> suggest using a
>  >force field that others have used for such solid materials, like 
> nanotubes or
>  >other graphene surfaces. Otherwise, you will have to somehow 
> demonstrate that a
>  >force field designed for use with condensed phase biomolecules is 
> applicable to
>  >your gas-phase graphene lattice.
>  >
>  >> The graphene lattice is only vibrating slightly and looks like a 
> bunch of
>  >> travelling waves.
>  >>
>  >> I believe I am using proper dihedrals and not improper dihedrals in my
>  >> model.
>  >>
>  >
>  >It would seem. Consider if impropers might be necessary to keep your 
> planar
>  >groups planar. That's what they are there for.
>  >
>  >> Since the graphene structure will be connected to electrodes at both 
> ends
>  >> and will be mounted above a substrate, I assume the atoms in the
>  >> structure are not completely free and thus I need to model them being
>  >> restricted in their movement. Maybe position restraints are more
>  >> appropriate than freezing to model such a situation.
>  >>
>  >> I do not see anything in the trajectory that provides clues as to what
>  >> might be causing the segmentation fault.
>  >>
>  >
>  >Then it will be very difficult to get any more remote help ;) If you
>  >consistently get the crash between step 20,000 and 30,000, then 
> perhaps split
>  >your simulation into shorter sections, and during the time when you 
> expect the
>  >crash to occur, set nstxtcout = (some small value, like 1 or 10) to 
> obtain the
>  >most detail possible. At some point, something is going to go 
> careening off
>  >into infinity.
>  >
>  >-Justin
>  >
>  >> Thanks again for your help.
>  >>
>  >> Darrell
>  >>
>  >>> Date: Fri, 17 Jul 2009 19:08:38 -0400
>  >>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>  >>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>  >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >>> Message-ID: <4A610476.2090709 at vt.edu>
>  >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >>>
>  >>>
>  >>>
>  >>> darrellk at ece.ubc.ca wrote:
>  >>>> Hi Justin,
>  >>>> I froze the graphene sheet because, prior to freezing it, I 
> noticed that
>  >>>> it was vibrating and thought that maybe its vibration was not 
> allowing
>  >>>> the NH3 molecules to adsorb (bond) to it. But after freezing the
>  >>>> graphene sheet, I see that see that NH3 molecules are still not 
> bonding
>  >>>> to it. Physical experiments of NH3 and a graphene lattice 
> connected to
>  >>>> electrodes have shown that NH3 does adsorb to graphene, but all I see
>  >>>> are NH3 molecules coming close to the graphene surface and then 
> bouncing
>  >>>> away which I am assuming is a result of repulsion between the 
> negatively
>  >>>> charged N atom in the ammonia molecule and the pi electrons in the
>  >>>> graphene lattice. So I am not sure why experiments have shown 
> adsorption
>  >>>> unless adsoption is occurring as a result of a current flowing 
> through
>  >>>> the graphene structure or as a result of edge effects at the 
> interface
>  >>>> between the electrodes and the graphene lattice.
>  >>>>
>  >>> What parameters are you using for the species involved? Could be 
> that there's
>  >>> something wrong with your model.
>  >>>
>  >>>> Could you tell me how freezing is different that position 
> restraining as
>  >>>> this is not completely clear to me?
>  >>>>
>  >>> Freezing means positions are absolutely fixed and never updated. 
> Position
>  >>> restraining means there is an energy penalty to movement, but 
> positions can
>  >>> adjust slightly. I was thinking that if you have some strange 
> interaction
>  >>> happening, and freezing was preventing any reaction to the force, 
> then you'd see
>  >>> an explosion. I don't necessarily see why you need to apply either, 
> but that
>  >>> will depend on the extent of "vibration" that you see in the 
> graphene sheet.
>  >>> Are you applying improper dihedrals appropriately? Are the rings 
> puckering, or
>  >>> just vibrating slightly (which could be normal)?
>  >>>
>  >>>> I will try position restraining the graphene structure and see if 
> that
>  >>>> resolves my problem.
>  >>>>
>  >>>> I have been able to view a trajectory for simulations of fewer than
>  >>>> 20,000 time steps and see the frozen graphene lattice and the NH3
>  >>>> molecules floating through space.
>  >>>>
>  >>>> Note that the segmentation fault only occurs sometime between 
> 20,000 and
>  >>>> 30,000 time steps. Could it be that the "funky" behaviour associated
>  >>>> with freezing would take 20,000+ time steps to cause a segmentation
>  >>>> fault?
>  >>>>
>  >>> Depends entirely upon what's causing the explosion. Any clues from 
> the trajectory?
>  >>>
>  >>> -Justin
>  >>>
>  >>>> Thanks again for your help.
>  >>>>
>  >>>> Darrell
>  >>>>
>  >>>>> Date: Thu, 16 Jul 2009 16:20:04 -0400
>  >>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>  >>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>  >>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >>>>> Message-ID: <4A5F8B74.6070404 at vt.edu>
>  >>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >>>>>
>  >>>>>
>  >>>>>
>  >>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>> Hi Justin,
>  >>>>>> Thanks for the explanation of the difference between EM & 
> equilibration.
>  >>>>>> Since in my model, I: (i) only have the graphene sheet and ammonia
>  >>>>>> molecules spaced reasonably far apart from each other (1332 NH3
>  >>>>>> molecules in a 38x38x38 box) and from the graphene sheet (distance
>  >>>>>> between the closest ammonia molecule and the graphene sheet is 
> greater
>  >>>>>> than the molecular diameter of ammonia - maybe this is too close 
> and
>  >>>>>> could be causing my problem?); (ii) freeze the graphene sheet; I am
>  >>>>>> thinking equilibration is not required in my model. Please let 
> me know
>  >>>>>> if you think I still need to perform equilibration.
>  >>>>>>
>  >>>>>> Yes, the EM did converge satisfactorily. Here is the output from 
> EM:
>  >>>>>> Steepest Descents converged to Fmax < 250 in 61 steps
>  >>>>>> Potential Energy = 4.6094102e+04
>  >>>>>> Maximum force = 2.4543298e+02 on atom 1
>  >>>>>> Norm of force = 7.5803179e+03
>  >>>>>>
>  >>>>>> Is this a reasonable value for FMax?
>  >>>>>>
>  >>>>> Your Fmax looks fine. Why is it necessary to freeze the graphene 
> sheet? Why
>  >>>>> not use position restraints (to rule out funky behavior of being 
> frozen)?
>  >>>>>
>  >>>>> Did you ever obtain a trajectory with enough frames that you 
> could watch? What
>  >>>>> happened?
>  >>>>>
>  >>>>> -Justin
>  >>>>>
>  >>>>>> Thanks again for your help.
>  >>>>>>
>  >>>>>> Darrell
>  >>>>>>
>  >>>>>>
>  >>>>>>> Date: Thu, 16 Jul 2009 07:15:12 -0400
>  >>>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>  >>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>  >>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >>>>>>> Message-ID: <4A5F0BC0.4020200 at vt.edu>
>  >>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >>>>>>>
>  >>>>>>>
>  >>>>>>>
>  >>>>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>>>> Hi Mark,
>  >>>>>>>> I do not do any equilibration, I only do energy minimization 
> as in the
>  >>>>>>>> "GROMACS Tutorial for Solvation Study of Spider Toxin 
> Peptide". Please
>  >>>>>>>> let me know if I need to do equilibration and what is the 
> difference
>  >>>>>>>> between energy minimization and equilibration as this is not 
> clear to me.
>  >>>>>>>>
>  >>>>>>> Did the EM converge satisfactorily? What was Fmax?
>  >>>>>>>
>  >>>>>>> Unlike EM, equilibration is an MD process; for a protein 
> system, one generally
>  >>>>>>> position-restrains the protein and allows the surrounding 
> solvent to optimize
>  >>>>>>> around the structure.
>  >>>>>>>
>  >>>>>>> -Justin
>  >>>>>>>
>  >>>>>>>> Here is an mdp file for a run that actually completed 
> successfully:
>  >>>>>>>> title =Graphene
>  >>>>>>>> ;warnings =10
>  >>>>>>>> cpp =cpp
>  >>>>>>>> ;define =-DPOSRES
>  >>>>>>>> constraints =none
>  >>>>>>>> integrator =md
>  >>>>>>>> dt =0.002 ; ps
>  >>>>>>>> nsteps =10000
>  >>>>>>>> nstcomm =100
>  >>>>>>>> nstxout =100
>  >>>>>>>> ;nstvout =1000
>  >>>>>>>> nstfout =0
>  >>>>>>>> nstlog =100
>  >>>>>>>> nstenergy =100
>  >>>>>>>> nstlist =100
>  >>>>>>>> ns_type =grid
>  >>>>>>>> rlist =2.0
>  >>>>>>>> coulombtype =PME
>  >>>>>>>> rcoulomb =2.0
>  >>>>>>>> vdwtype =cut-off
>  >>>>>>>> rvdw =5.0
>  >>>>>>>> fourierspacing =0.12
>  >>>>>>>> fourier_nx =0
>  >>>>>>>> fourier_ny =0
>  >>>>>>>> fourier_nz =0
>  >>>>>>>> pme_order =4
>  >>>>>>>> ewald_rtol =1e-5
>  >>>>>>>> optimize_fft =yes
>  >>>>>>>>
>  >>>>>>>> ; This section freezes graphene lattice
>  >>>>>>>> energygrps = Grph NH3
>  >>>>>>>> energygrp_excl = Grph Grph
>  >>>>>>>> freezegrps = Grph ; Freeze graphene lattice
>  >>>>>>>> freezedim = Y Y Y; in all directions
>  >>>>>>>>
>  >>>>>>>> Tcoupl =berendsen
>  >>>>>>>> tau_t =0.5 0.5
>  >>>>>>>> tc-grps =NH3 Grph
>  >>>>>>>> ref_t =300 300
>  >>>>>>>>
>  >>>>>>>> ;coupl = parrinello-rahman
>  >>>>>>>> ;tau_p = 1.5
>  >>>>>>>> ;compressibility = 1.3
>  >>>>>>>> ;ref_p = 0.061
>  >>>>>>>>
>  >>>>>>>> gen_vel = yes
>  >>>>>>>> gen_temp = 300.0
>  >>>>>>>> gen_seed = 173529
>  >>>>>>>>
>  >>>>>>>> And here is a copy of an mdp file for a run that did not complete
>  >>>>>>>> successfully:
>  >>>>>>>>
>  >>>>>>>> title =Graphene
>  >>>>>>>> ;warnings =10
>  >>>>>>>> cpp =cpp
>  >>>>>>>> ;define =-DPOSRES
>  >>>>>>>> constraints =none
>  >>>>>>>> integrator =md
>  >>>>>>>> dt =0.002 ; ps
>  >>>>>>>> nsteps =30000
>  >>>>>>>> nstcomm =500
>  >>>>>>>> nstxout =500
>  >>>>>>>> ;nstvout =1000
>  >>>>>>>> nstfout =0
>  >>>>>>>> nstlog =500
>  >>>>>>>> nstenergy =500
>  >>>>>>>> nstlist =500
>  >>>>>>>> ns_type =grid
>  >>>>>>>> rlist =2.0
>  >>>>>>>> coulombtype =PME
>  >>>>>>>> rcoulomb =2.0
>  >>>>>>>> vdwtype =cut-off
>  >>>>>>>> rvdw =5.0
>  >>>>>>>> fourierspacing =0.12
>  >>>>>>>> fourier_nx =0
>  >>>>>>>> fourier_ny =0
>  >>>>>>>> fourier_nz =0
>  >>>>>>>> pme_order =4
>  >>>>>>>> ewald_rtol =1e-5
>  >>>>>>>> optimize_fft =yes
>  >>>>>>>>
>  >>>>>>>> ; This section freezes graphene lattice
>  >>>>>>>> energygrps = Grph NH3
>  >>>>>>>> energygrp_excl = Grph Grph
>  >>>>>>>> freezegrps = Grph ; Freeze graphene lattice
>  >>>>>>>> freezedim = Y Y Y; in all directions
>  >>>>>>>>
>  >>>>>>>> Tcoupl =berendsen
>  >>>>>>>> tau_t =0.5 0.5
>  >>>>>>>> tc-grps =NH3 Grph
>  >>>>>>>> ref_t =300 300
>  >>>>>>>>
>  >>>>>>>> ;coupl = parrinello-rahman
>  >>>>>>>> ;tau_p = 1.5
>  >>>>>>>> ;compressibility = 1.3
>  >>>>>>>> ;ref_p = 0.061
>  >>>>>>>>
>  >>>>>>>> gen_vel = yes
>  >>>>>>>> gen_temp = 300.0
>  >>>>>>>> gen_seed = 173529
>  >>>>>>>>
>  >>>>>>>> Please let me know what you think might be the problem.
>  >>>>>>>>
>  >>>>>>>> Thanks
>  >>>>>>>>
>  >>>>>>>> Darrell
>  >>>>>>>>
>  >>>>>>>>> Date: Thu, 16 Jul 2009 09:47:49 +1000
>  >>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>  >>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>  >>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >>>>>>>>> Message-ID: <4A5E6AA5.4040809 at anu.edu.au>
>  >>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >>>>>>>>>
>  >>>>>>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>>>>>> Hi Mark,
>  >>>>>>>>>> Yes, I know that the box dimensions are defined in the last 
> line of the
>  >>>>>>>>>> .gro file and I have defined these dimensions as 38 nm x 38 
> nm x 38 nm
>  >>>>>>>>>> in the .gro file.
>  >>>>>>>>> OK.
>  >>>>>>>>>
>  >>>>>>>>>> I looked through my .gro file to ensure none of the atoms 
> had coordinates
>  >>>>>>>>>> outside the 38x38x38 box. While I was reviewing the file I 
> did notice
>  >>>>>>>>>> that some coordinates had negative values, slightly 
> negative, but
>  >>>>>>>>>> negative none the less. Could this be causing the 
> segmentation fault
>  >>>>>>>>>> between time step 10,000 and time step 30,000? Why wouldn't the
>  >>>>>>>>>> negative coordinates cause a segmentation fault much earlier?
>  >>>>>>>>> The absolute value of the coordinates is irrelevant.
>  >>>>>>>>>
>  >>>>>>>>> Your choice of 2.0 for rcoulomb is likely suboptimal for PME. 
> Some
>  >>>>>>>>> smaller value is probably more efficient, but this will not 
> be the cause
>  >>>>>>>>> of your problem.
>  >>>>>>>>>
>  >>>>>>>>> What is your system preparation regime? (i.e. EM + 
> equilibration)
>  >>>>>>>>>
>  >>>>>>>>> Can you post a corrected and current .mdp file?
>  >>>>>>>>>
>  >>>>>>>>> Mark
>  >>>>>>>>>
>  >>>>>>>>>>> Date: Wed, 15 Jul 2009 16:59:21 +1000
>  >>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>  >>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not 
> mapped)
>  >>>>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>  >>>>>>>>>>> Message-ID: <4A5D7E49.9020700 at anu.edu.au>
>  >>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >>>>>>>>>>>
>  >>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>>>>>>>> Hi Justin,
>  >>>>>>>>>>>> I was experiencing the problem before someone suggested 
> using editconf so
>  >>>>>>>>>>>> I do not think the problem is being caused by editconf. 
> But anyway here
>  >>>>>>>>>>>> is my editconf command. Let me know if you a source of 
> error in this
>  >>>>>>>>>>>> command line.
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> editconf -f graphene.gro -n index.ndx -o graphene_ec.gro
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> I did not want to add in additional space between the 
> solvent and the box
>  >>>>>>>>>>>> as I saw no reason for doing so. And hence that is why I 
> originally did
>  >>>>>>>>>>>> not use editconf.
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> My box dimensions are 38nm x 38nm x 38nm.
>  >>>>>>>>>>> The box dimensions are defined in the bottom line of the 
> .gro file, and
>  >>>>>>>>>>> not by the positions of the atoms in that file. If you 
> haven't ever set
>  >>>>>>>>>>> them to be suitable for your coordinates with editconf, 
> then they might
>  >>>>>>>>>>> not be.
>  >>>>>>>>>>>
>  >>>>>>>>>>> Mark
>  >>>>>>>>>>>
>  >>>>>>>>>>> I used cutoffs of 2 nm & 5 nm
>  >>>>>>>>>>>> for my system so ensure the cutoff occured at a distance 
> where the
>  >>>>>>>>>>>> potentials were stabalized (not changing). I guess I could 
> use shorter
>  >>>>>>>>>>>> cutoffs such as 1.5 nm & 2 nm and this may decrease my 
> computation time.
>  >>>>>>>>>>>> I also thought that I needed to use larger cut-offs since 
> I am dealing
>  >>>>>>>>>>>> in the gas phase and there is greater ditance between the 
> atoms in my
>  >>>>>>>>>>>> simulation than in liquid-based simulations.
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> In the .log files, I do not see any LINCS warnings or 
> neighborlist
>  >>>>>>>>>>>> errors.
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> I ran gmxcheck on a .trr file and was presented with the 
> following
>  >>>>>>>>>>>> output:
>  >>>>>>>>>>>> *********************************************
>  >>>>>>>>>>>> Checking file mdtraj.trr
>  >>>>>>>>>>>> trn version: GMX_trn_file (single precision)
>  >>>>>>>>>>>> Reading frame 0 time 0.000
>  >>>>>>>>>>>> # Atoms 10482
>  >>>>>>>>>>>> Last frame 5 time 1.000
>  >>>>>>>>>>>>
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> Item #frames Timestep (ps)
>  >>>>>>>>>>>> Step 6 0.2
>  >>>>>>>>>>>> Time 6 0.2
>  >>>>>>>>>>>> Lambda 6 0.2
>  >>>>>>>>>>>> Coords 6 0.2
>  >>>>>>>>>>>> Velocities 6 0.2
>  >>>>>>>>>>>> Forces 0
>  >>>>>>>>>>>> Box 6 0.2
>  >>>>>>>>>>>> *********************************************
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> I ran two additional simulations with different values for 
> nsteps and
>  >>>>>>>>>>>> nstxxxx paramaters and have the following to report:
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> When I run a simulation with the following parameters it 
> completes
>  >>>>>>>>>>>> successfully and I see, in the log file, the system output 
> every 100
>  >>>>>>>>>>>> time steps.
>  >>>>>>>>>>>> nsteps =10000
>  >>>>>>>>>>>> nstcomm =100
>  >>>>>>>>>>>> nstxout =100
>  >>>>>>>>>>>> nstfout =0
>  >>>>>>>>>>>> nstlog =100
>  >>>>>>>>>>>> nstenergy =100
>  >>>>>>>>>>>> nstlist =100
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> When I run a simulation with the following parameters it 
> fails with a
>  >>>>>>>>>>>> sementation fault and, in the log file, I do not see 
> system output every
>  >>>>>>>>>>>> 500 time steps.
>  >>>>>>>>>>>> nsteps =30000
>  >>>>>>>>>>>> nstcomm =500
>  >>>>>>>>>>>> nstxout =500
>  >>>>>>>>>>>> nstfout =0
>  >>>>>>>>>>>> nstlog =500
>  >>>>>>>>>>>> nstenergy =500
>  >>>>>>>>>>>> nstlist =500
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> Please let me know what you think might be the problem.
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> Thank you very much.
>  >>>>>>>>>>>>
>  >>>>>>>>>>>> Darrell
>  >>>>>>>>>>>>
>  >>>>>>>>>>>>
>  >>>>>>>>>>>>> Date: Mon, 13 Jul 2009 15:37:15 -0400
>  >>>>>>>>>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>  >>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not 
> mapped)
>  >>>>>>>>>>>>> To: Discussion list for GROMACS users 
> <gmx-users at gromacs.org>
>  >>>>>>>>>>>>> Message-ID: <4A5B8CEB.4020609 at vt.edu>
>  >>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>>>>>>>>>> Hi Mark,
>  >>>>>>>>>>>>>> I used editconf on my .gro file with zero space between 
> my solvent and
>  >>>>>>>>>>>>>> the box and the resulting box had the exact same 
> dimension as the
>  >>>>>>>>>>>>>> initial box. I also performed a number of simulation 
> runs with different
>  >>>>>>>>>>>>> If you're using editconf to define zero space, what's the 
> point? I only ask
>  >>>>>>>>>>>>> because it is a potential source of error if you think 
> you're adding zero space,
>  >>>>>>>>>>>>> but something else might be going on. Maybe you can post 
> your editconf command
>  >>>>>>>>>>>>> line.
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>> What are your box dimensions? Are cut-off lengths of 2.0 
> and 5.0 nm appropriate
>  >>>>>>>>>>>>> for your system? How did you determine that these 
> cut-off's should be used?
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>>> mdp parameters hoping this would provide me some 
> indication of the cause
>  >>>>>>>>>>>>>> of the fault but to no avail. I looked through the log 
> files, error
>  >>>>>>>>>>>>>> files, and output files and could not find any output to 
> help me
>  >>>>>>>>>>>>>> identify the source of my error.
>  >>>>>>>>>>>>>>
>  >>>>>>>>>>>>> It is very odd that Gromacs isn't report anything at all. 
> No LINCS warnings?
>  >>>>>>>>>>>>> No neighborlist errors? These would be in the .log file.
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>>> Could you please let me know how I can look at my 
> structure at each point
>  >>>>>>>>>>>>>> as you indicate below as I do not see any files output 
> that provide me
>  >>>>>>>>>>>>>> to do so? I tried to look at the .trr file but when I 
> try to load it
>  >>>>>>>>>>>>>> into VMD, it causes an error. I am assuming this error 
> is caused because
>  >>>>>>>>>>>>>> the .trr file did not complete correctly due to the 
> segmentation fault.
>  >>>>>>>>>>>>>> Please advise.
>  >>>>>>>>>>>>>>
>  >>>>>>>>>>>>> How early is the segmentation fault occurring? I have 
> found it useful sometimes
>  >>>>>>>>>>>>> to set nstxout (or nstxtcout) = 1 to try to catch the 
> first few frames if the
>  >>>>>>>>>>>>> explosion is occurring early. In any case, gmxcheck will 
> help determine how
>  >>>>>>>>>>>>> many frames are present, as well as the integrity of the 
> file (broken frames, etc).
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>> -Justin
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>>> Thanks.
>  >>>>>>>>>>>>>>
>  >>>>>>>>>>>>>> Darrell
>  >>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>> Date: Tue, 07 Jul 2009 09:19:42 +1000
>  >>>>>>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>  >>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address 
> not mapped)
>  >>>>>>>>>>>>>>> To: Discussion list for GROMACS users 
> <gmx-users at gromacs.org>
>  >>>>>>>>>>>>>>> Message-ID: <4A52868E.6010807 at anu.edu.au>
>  >>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; 
> format=flowed
>  >>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>>>>>>>>>>>> Hi Mark,
>  >>>>>>>>>>>>>>>> I added the energy group exclusions as indicated in 
> your previous
>  >>>>>>>>>>>>>>>> response but am still experiencing the same problem. I 
> looked at the
>  >>>>>>>>>>>>>>>> .log files and see that in one log file it tells me 
> that my box is
>  >>>>>>>>>>>>>>>> exploding. However, I do not have many molecules in my 
> simulation and
>  >>>>>>>>>>>>>>>> therefore do not think that it is possible that my box 
> is exploding from
>  >>>>>>>>>>>>>>>> pressure.
>  >>>>>>>>>>>>>>> Sure, but if there's something malformed with your 
> model physics or
>  >>>>>>>>>>>>>>> starting configuration, then large forces can make 
> anything explode.
>  >>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>> Look at your structures at each point and see where 
> things start to go
>  >>>>>>>>>>>>>>> wrong. Make sure you've used editconf on your starting 
> structure to
>  >>>>>>>>>>>>>>> provide the right box dimensions.
>  >>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>> Mark
>  >>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>> Maybe if I re-state my simulation it will help you in 
> providing me
>  >>>>>>>>>>>>>>>> direction on what might be causing the problem. My 
> simulation consists
>  >>>>>>>>>>>>>>>> of a graphene lattice with a layer of ammonia 
> molecules above it. The
>  >>>>>>>>>>>>>>>> box is very large and there is lots of empty space in 
> the box. So I am a
>  >>>>>>>>>>>>>>>> little confused as to how the box could be exploding.
>  >>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>> Thanks again in advance for your help.
>  >>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>> Darrell Koskinen
>  >>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>> Date: Fri, 03 Jul 2009 11:41:45 +1000
>  >>>>>>>>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>  >>>>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address 
> not mapped)
>  >>>>>>>>>>>>>>>>> To: Discussion list for GROMACS users 
> <gmx-users at gromacs.org>
>  >>>>>>>>>>>>>>>>> Message-ID: <4A4D61D9.6080700 at anu.edu.au>
>  >>>>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; 
> format=flowed
>  >>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>  >>>>>>>>>>>>>>>>>> Dear GROMACS Gurus,
>  >>>>>>>>>>>>>>>>>> I am experiencing a segmentation fault when mdrun 
> executes. My simulation
>  >>>>>>>>>>>>>>>>>> has a graphene lattice with an array (layer) of 
> ammonia molecules above
>  >>>>>>>>>>>>>>>>>> it. The box is three times the width of the graphene 
> lattice, three
>  >>>>>>>>>>>>>>>>>> times the length of the graphene lattice, and three 
> times the height
>  >>>>>>>>>>>>>>>>>> between the graphene lattice and the ammonia 
> molecules. I am including
>  >>>>>>>>>>>>>>>>>> the mdp file and the error message.
>  >>>>>>>>>>>>>>>>> Probably your system is exploding when integration 
> fails with excessive
>  >>>>>>>>>>>>>>>>> forces. You should look at the bottom of stdout, 
> stderr, *and* the .log
>  >>>>>>>>>>>>>>>>> file to diagnose. The error message you give below is 
> merely the
>  >>>>>>>>>>>>>>>>> diagnostic trace from the MPI library, and it not 
> useful for finding out
>  >>>>>>>>>>>>>>>>> what GROMACS thinks the problem might be. Further 
> advice below.
>  >>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> 
> ***************************************************************************
>  >>>>>>>>>>>>>>>>>> .mdp file
>  >>>>>>>>>>>>>>>>>> title =FWS
>  >>>>>>>>>>>>>>>>>> ;warnings =10
>  >>>>>>>>>>>>>>>>>> cpp =cpp
>  >>>>>>>>>>>>>>>>>> ;define =-DPOSRES
>  >>>>>>>>>>>>>>>>>> ;constraints =all-bonds
>  >>>>>>>>>>>>>>>>>> integrator =md
>  >>>>>>>>>>>>>>>>>> dt =0.002 ; ps
>  >>>>>>>>>>>>>>>>>> nsteps =100000
>  >>>>>>>>>>>>>>>>>> nstcomm =1000
>  >>>>>>>>>>>>>>>>>> nstxout =1000
>  >>>>>>>>>>>>>>>>>> ;nstvout =1000
>  >>>>>>>>>>>>>>>>>> nstfout =0
>  >>>>>>>>>>>>>>>>>> nstlog =1000
>  >>>>>>>>>>>>>>>>>> nstenergy =1000
>  >>>>>>>>>>>>>>>>>> nstlist =1000
>  >>>>>>>>>>>>>>>>>> ns_type =grid
>  >>>>>>>>>>>>>>>>>> rlist =2.0
>  >>>>>>>>>>>>>>>>>> coulombtype =PME
>  >>>>>>>>>>>>>>>>>> rcoulomb =2.0
>  >>>>>>>>>>>>>>>>>> vdwtype =cut-off
>  >>>>>>>>>>>>>>>>>> rvdw =5.0
>  >>>>>>>>>>>>>>>>>> fourierspacing =0.12
>  >>>>>>>>>>>>>>>>>> fourier_nx =0
>  >>>>>>>>>>>>>>>>>> fourier_ny =0
>  >>>>>>>>>>>>>>>>>> fourier_nz =0
>  >>>>>>>>>>>>>>>>>> pme_order =4
>  >>>>>>>>>>>>>>>>>> ewald_rtol =1e-5
>  >>>>>>>>>>>>>>>>>> optimize_fft =yes
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> ; This section added in to freeze hydrogen atoms at 
> edge of graphene
>  >>>>>>>>>>>>>>>>>> lattice to prevent movement of lattice
>  >>>>>>>>>>>>>>>>>> ;energygrp_excl = Edge Edge Edge Grph Grph Grph
>  >>>>>>>>>>>>>>>>>> freezegrps = Edge Grph ; Hydrogen atoms in graphene 
> lattice are
>  >>>>>>>>>>>>>>>>>> associated with the residue Edge
>  >>>>>>>>>>>>>>>>> See comments in 7.3.24 of manual. You need the energy 
> group exclusions.
>  >>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>> Mark
>  >>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in 
> all directions
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> ;Tcoupl =berendsen
>  >>>>>>>>>>>>>>>>>> ;tau_t =0.1 0.1
>  >>>>>>>>>>>>>>>>>> ;tc-grps =protein non-protein
>  >>>>>>>>>>>>>>>>>> ;ref_t = 300 300
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> ;Pcoupl = parrinello-rahman
>  >>>>>>>>>>>>>>>>>> ;tau_p = 0.5
>  >>>>>>>>>>>>>>>>>> ;compressibility = 4.5e-5
>  >>>>>>>>>>>>>>>>>> ;ref_p = 1.0
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> ;gen_vel = yes
>  >>>>>>>>>>>>>>>>>> ;gen_temp = 300.0
>  >>>>>>>>>>>>>>>>>> ;gen_seed = 173529
>  >>>>>>>>>>>>>>>>>> 
> ***************************************************************************
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> 
> ***************************************************************************
>  >>>>>>>>>>>>>>>>>> ERROR IN OUTPUT FILE
>  >>>>>>>>>>>>>>>>>> [node16:25758] *** Process received signal ***
>  >>>>>>>>>>>>>>>>>> [node16:25758] Signal: Segmentation fault (11)
>  >>>>>>>>>>>>>>>>>> [node16:25758] Signal code: Address not mapped (1)
>  >>>>>>>>>>>>>>>>>> [node16:25758] Failing at address: 0xfffffffe1233e230
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 0] /lib64/libpthread.so.0 
> [0x3834a0de80]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 1] 
> /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6)
>  >>>>>>>>>>>>>>>>>> [0x2ba295dd0606]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 2] 
> /usr/lib64/libmd_mpi.so.4(do_pme+0x808)
>  >>>>>>>>>>>>>>>>>> [0x2ba295dd4058]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 3] 
> /usr/lib64/libmd_mpi.so.4(force+0x8de)
>  >>>>>>>>>>>>>>>>>> [0x2ba295dba5be]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 4] 
> /usr/lib64/libmd_mpi.so.4(do_force+0x5ef)
>  >>>>>>>>>>>>>>>>>> [0x2ba295ddeaff]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40) 
> [0x4142f0]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 8] 
> /lib64/libc.so.6(__libc_start_main+0xf4)
>  >>>>>>>>>>>>>>>>>> [0x3833e1d8b4]
>  >>>>>>>>>>>>>>>>>> [node16:25758] [ 9] mdrun_mpi [0x40429a]
>  >>>>>>>>>>>>>>>>>> [node16:25758] *** End of error message ***
>  >>>>>>>>>>>>>>>>>> mpirun noticed that job rank 7 with PID 25758 on 
> node node16 exited on
>  >>>>>>>>>>>>>>>>>> signal 11 (Segmentation fault).
>  >>>>>>>>>>>>>>>>>> 7 processes killed (possibly by Open MPI)
>  >>>>>>>>>>>>>>>>>> 
> ***************************************************************************
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> Could you please let me know what you think may be 
> causing the fault?
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> Much thanks in advance.
>  >>>>>>>>>>>>>>>>>>
>  >>>>>>>>>>>>>>>>>> Darrell Koskinen
>  >>>>>>>>>>>>>> _______________________________________________
>  >>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>  >>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>  >>>>>>>>>>>>>> Please search the archive at 
> http://www.gromacs.org/search before posting!
>  >>>>>>>>>>>>>> Please don't post (un)subscribe requests to the list. 
> Use the
>  >>>>>>>>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>  >>>>>>>>>>>>>> Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php
>  >>>>>>>>>>>>>>
>  >>>>>>>>>>>>> --
>  >>>>>>>>>>>>> ========================================
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>> Justin A. Lemkul
>  >>>>>>>>>>>>> Ph.D. Candidate
>  >>>>>>>>>>>>> ICTAS Doctoral Scholar
>  >>>>>>>>>>>>> Department of Biochemistry
>  >>>>>>>>>>>>> Virginia Tech
>  >>>>>>>>>>>>> Blacksburg, VA
>  >>>>>>>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>  >>>>>>>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>  >>>>>>>>>>>>>
>  >>>>>>>>>>>>> ========================================
>  >>>>>>>>>>>> _______________________________________________
>  >>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>  >>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>  >>>>>>>>>>>> Please search the archive at http://www.gromacs.org/search 
> before posting!
>  >>>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>  >>>>>>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>  >>>>>>>>>>>> Can't post? Read 
> http://www.gromacs.org/mailing_lists/users.php
>  >>>>>>>>>>>>
>  >>>>>>>>>>> ------------------------------
>  >>>>>>>>>>>
>  >>>>>>>>>>> _______________________________________________
>  >>>>>>>>>>> gmx-users mailing list
>  >>>>>>>>>>> gmx-users at gromacs.org
>  >>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>  >>>>>>>>>>> Please search the archive at http://www.gromacs.org/search 
> before posting!
>  >>>>>>>>>>>
>  >>>>>>>>>>> End of gmx-users Digest, Vol 63, Issue 61
>  >>>>>>>>>>> *****************************************
>  >>>>>>>>>>>
>  >>>>>>>>>> _______________________________________________
>  >>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>  >>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>  >>>>>>>>>> Please search the archive at http://www.gromacs.org/search 
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>  >>>>>>>>>>
>  >>>>>>>> _______________________________________________
>  >>>>>>>> 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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>  >>>>>>>> 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
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>  >>>>>> 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!
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>  >> 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!
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> 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

========================================