[gmx-users] Segmentation Fault (Address not mapped)
Darrell Koskinen
darrellk at ece.ubc.ca
Tue Aug 4 03:50:23 CEST 2009
Hi Justin,
I just want to use the most appropriate force field and associated
parameters for my simulation of graphene in ammonia gas. Is OPLS an
appropriate force field to use?
I have searched for force fields for gas simulations but have not yet
been able to find one specific to graphene and ammonia gas. Since
graphene is in a condensed phase and ammonia is in a gas phase and I
understand that I need to use the same force field for both graphene and
ammonia, I will have to use a force field for either gas-phase MD or
condensed-phase MD. Since I am finding it difficult to locate gas-phase
MD force fields, is it acceptable to use a condensed-phase MD force
field, which I believe is the case for OPLS (please confirm)?
If it is acceptable to use OPLS, then I am assuming that I am to use the
parameters in the ffoplsaabon.itp and ffoplsaanb.itp as is and not
modify them (i.e. not create frankenstein force fields), correct? Am I
correct in my understanding that the only item that requires
modification is the .n2t file?
And, by the way, I have resolved the segmentation fault problem. It was
being caused by the freezing of the graphene lattice. When I removed the
freezing, I saw the graphene structure curl upward and am thinking that
by freezing the atoms in place it was creating great forces between the
atoms as they were kept from moving into their preferred orientation.
I subsequently tried to restrain the atoms via position restraints, but
I still see the graphene structure moving. Could you please let me know
why the position restraints do not appear to be working? Do I need to
use greater restraint parameters? I created a position restaint file for
the graphene structure posre.itp using "genpr -f graphene.gro -n
index.ndx -o posre.itp -fc 0 0 1000" (note that genrestr is not
recognized in my version of GROMACS) to restrain the graphene lattice to
the x-y plane and submitted 2 runs with the following in my run.mdp file:
Run 1:
define =-DPOSRES
constraints =none
Run 2:
define =-DPOSRES
constraints =all-bonds
Run 1 with constraints=none appears to restrain the graphene lattice
better than the Run 2 with constraints=all-bonds.
Here is an extract from posre.itp for the first few atoms:
******************************************
; position restraints for Grph of Ãzú^K^Q+
[ position_restraints ]
; i funct fcx fcy fcz
1 1 0 0 1000
2 1 0 0 1000
3 1 0 0 1000
******************************************
Again, I thank you very much for your assistance.
Darrell
> Date: Mon, 27 Jul 2009 17:48:02 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A6E2092.402 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> Darrell Koskinen wrote:
>
>> Hi Justin,
>> With regard to your comment about using other force fields for my
>> simulation of graphene surrounded by ammonia gas, are referring to the
>> force fields for both graphene and ammonia or only to the force field
>> for graphene?
>>
>>
>
> The "force field" should be one in the same. The parameters should be suitably
> derived using the same scheme as the original work.
>
>
>> I reviewed my selection of the force field parameters for graphene and
>> see that I selected the parameters from the paper by Cornell et al.
>> since a paper on deformation of carbon nanotubes ("A structural
>> mechanics approach for the analysis of carbon nanotubes" by Chunyu Li,
>> Tsu-Wei Chou in International Journal of Solids and Structures 40 (2003)
>> 2487–2499) used parameters from the paper by Cornell et al. Is this
>> sufficient to justify the use of these parameters? I also thought that
>> graphene and ammonia would be considered organic since they are
>> comprised of carbon, nitrogen, and hydrogen, which are all common
>> elements found in organic matter.
>>
>>
>
> If you feel that precedent is sufficient, then I guess go ahead. But realize
> that the paper by Cornell et al. refers to parameters suitable for simulations
> of proteins and nucleic acids, as well as a few organic functional groups.
> Parameterization was based on peptide backbone geometry, as well as other
> parameters, likely none of which involved graphene and gaseous ammonia (they
> were doing liquid simulations).
>
>
>> With regard to the parameters for ammonia, is it acceptable to use the
>> parameters from the paper by Cornell et al. or do I need to find papers
>> specifically related to ammonia gas molecular dynamics simulations?
>>
>>
>
> I would seriously consider finding parameters (if they exist) that have been
> derived for use with gas-phase simulations.
>
>
>> With regard to dihedral selection, I looked at the .top file and see
>> that the function type is listed as 3 in the dihedrals section, which I
>> believe indicates that my simulation is using a Ryckaert-Bellemans
>> function. It appears to me that if I am using the OPLS force field that
>> the Ryckaert-Bellemans dihedral type is automatically selected. I do see
>> in the ffoplsaabon.itp file that there is an improper dihedral
>> definition which think I could potentially use in my simulation
>> "improper_Z_CA_X_Y", but how do I cause my simulation to use this
>> definition? Do I need to add the following line to my .top file?
>> "#define improper_Z_CA_X_Y"
>>
>>
>
> No, you would have to use a special dihedrals section, that specifies the four
> atoms involved (function type 1), followed by the specification of that
> particular improper ("improper_Z_CA_X_Y"). See the manual for more details,
> and/or generate a topology for a protein with pdb2gmx with OPLS-AA and see how
> they're defined.
>
>
>> Further, I thought that I could simply modify the appropriate lines of
>> the ffoplsaanb.itp and ffoplsaabon.itp to enter in the parameters found
>> in the paper by Cornell et al. so that they will be used in my
>> simulation. Am I correct in my assumption?
>>
>>
>
> Modifying ffoplsaa files to parameters that are not OPLS-AA is probably a bad
> choice. If you're dead-set on using these parameters, download the ffamber
> ports and use the ffamber94 force field, not some Frankensteined-OPLS. Besides,
> all of the parameters in the Cornell paper are in kcal/mol/A^2, which will
> require conversion to Gromacs standard units. If you've printed them directly
> in your previous attempts, I can guarantee you you're not getting the values you
> think you are.
>
> -Justin
>
>
>> Thanks again for your help.
>>
>> Darrell
>>
>>
>> >Date: Fri, 17 Jul 2009 22:11:07 -0400
>> >From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> >To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >Message-ID: <4A612F3B.7060503 at vt.edu>
>> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >
>> >
>> >
>> >darrellk at ece.ubc.ca wrote:
>> >> Hi Justin,
>> >> I am using the ffoplsaabon.itp parameters for:
>> >> bonds (CA-CA, CA-CT, CA-HA, CT-HC, H-N3)
>> >> angles (CA-CA-CA, CA-CA-HA, CA-CT-HC, H-N3-H)
>> >> dihedrals (X-CA-CA-X, X-CA-CT-X)
>> >>
>> >> I am using the ffolpsaanb.itp VdW parameters for H & N3
>> >>
>> >> And I am using the VdW parameters found in the paper "A Second
>> >> Generation Force Field for the Simulation of Proteins, Nucleic Acids,
>> >> and Organic Molecules" for CA, HA, CT, & HC doing the conversion from
>> >> Angstroms (paper units) to nm (ffoplsaanb.itp units) for sigma and from
>> >> kcal/mol (paper units) to kJ/mol (ffoplsaanb.itp units) for epsilon.
>> The
>> >> converted parameters for sigma were different by only +/-2% to +/-8%
>> >> from the values in ffoplsaanb.itp, but the converted parameters for
>> >> epsilon were different by +/-23% to +/-66% from the values in
>> >> ffoplsaanb.itp. Is this a valid paper to use for selection of
>> parameters?
>> >>
>> >
>> >If memory serves, that paper is the derivation by Cornell, et al. for the
>> >AMBER94 parameter set, so no, you are not going to find those same
>> parameters in
>> >ffoplsaanb.itp.
>> >
>> >Furthermore, the title of the paper indicates that the parameters are for
>> >proteins, nucleic acids, and organic molecules. Has anyone else in the
>> >literature used these parameters for graphene lattices? I would
>> suggest using a
>> >force field that others have used for such solid materials, like
>> nanotubes or
>> >other graphene surfaces. Otherwise, you will have to somehow
>> demonstrate that a
>> >force field designed for use with condensed phase biomolecules is
>> applicable to
>> >your gas-phase graphene lattice.
>> >
>> >> The graphene lattice is only vibrating slightly and looks like a
>> bunch of
>> >> travelling waves.
>> >>
>> >> I believe I am using proper dihedrals and not improper dihedrals in my
>> >> model.
>> >>
>> >
>> >It would seem. Consider if impropers might be necessary to keep your
>> planar
>> >groups planar. That's what they are there for.
>> >
>> >> Since the graphene structure will be connected to electrodes at both
>> ends
>> >> and will be mounted above a substrate, I assume the atoms in the
>> >> structure are not completely free and thus I need to model them being
>> >> restricted in their movement. Maybe position restraints are more
>> >> appropriate than freezing to model such a situation.
>> >>
>> >> I do not see anything in the trajectory that provides clues as to what
>> >> might be causing the segmentation fault.
>> >>
>> >
>> >Then it will be very difficult to get any more remote help ;) If you
>> >consistently get the crash between step 20,000 and 30,000, then
>> perhaps split
>> >your simulation into shorter sections, and during the time when you
>> expect the
>> >crash to occur, set nstxtcout = (some small value, like 1 or 10) to
>> obtain the
>> >most detail possible. At some point, something is going to go
>> careening off
>> >into infinity.
>> >
>> >-Justin
>> >
>> >> Thanks again for your help.
>> >>
>> >> Darrell
>> >>
>> >>> Date: Fri, 17 Jul 2009 19:08:38 -0400
>> >>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> >>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> >>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >>> Message-ID: <4A610476.2090709 at vt.edu>
>> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >>>
>> >>>
>> >>>
>> >>> darrellk at ece.ubc.ca wrote:
>> >>>> Hi Justin,
>> >>>> I froze the graphene sheet because, prior to freezing it, I
>> noticed that
>> >>>> it was vibrating and thought that maybe its vibration was not
>> allowing
>> >>>> the NH3 molecules to adsorb (bond) to it. But after freezing the
>> >>>> graphene sheet, I see that see that NH3 molecules are still not
>> bonding
>> >>>> to it. Physical experiments of NH3 and a graphene lattice
>> connected to
>> >>>> electrodes have shown that NH3 does adsorb to graphene, but all I see
>> >>>> are NH3 molecules coming close to the graphene surface and then
>> bouncing
>> >>>> away which I am assuming is a result of repulsion between the
>> negatively
>> >>>> charged N atom in the ammonia molecule and the pi electrons in the
>> >>>> graphene lattice. So I am not sure why experiments have shown
>> adsorption
>> >>>> unless adsoption is occurring as a result of a current flowing
>> through
>> >>>> the graphene structure or as a result of edge effects at the
>> interface
>> >>>> between the electrodes and the graphene lattice.
>> >>>>
>> >>> What parameters are you using for the species involved? Could be
>> that there's
>> >>> something wrong with your model.
>> >>>
>> >>>> Could you tell me how freezing is different that position
>> restraining as
>> >>>> this is not completely clear to me?
>> >>>>
>> >>> Freezing means positions are absolutely fixed and never updated.
>> Position
>> >>> restraining means there is an energy penalty to movement, but
>> positions can
>> >>> adjust slightly. I was thinking that if you have some strange
>> interaction
>> >>> happening, and freezing was preventing any reaction to the force,
>> then you'd see
>> >>> an explosion. I don't necessarily see why you need to apply either,
>> but that
>> >>> will depend on the extent of "vibration" that you see in the
>> graphene sheet.
>> >>> Are you applying improper dihedrals appropriately? Are the rings
>> puckering, or
>> >>> just vibrating slightly (which could be normal)?
>> >>>
>> >>>> I will try position restraining the graphene structure and see if
>> that
>> >>>> resolves my problem.
>> >>>>
>> >>>> I have been able to view a trajectory for simulations of fewer than
>> >>>> 20,000 time steps and see the frozen graphene lattice and the NH3
>> >>>> molecules floating through space.
>> >>>>
>> >>>> Note that the segmentation fault only occurs sometime between
>> 20,000 and
>> >>>> 30,000 time steps. Could it be that the "funky" behaviour associated
>> >>>> with freezing would take 20,000+ time steps to cause a segmentation
>> >>>> fault?
>> >>>>
>> >>> Depends entirely upon what's causing the explosion. Any clues from
>> the trajectory?
>> >>>
>> >>> -Justin
>> >>>
>> >>>> Thanks again for your help.
>> >>>>
>> >>>> Darrell
>> >>>>
>> >>>>> Date: Thu, 16 Jul 2009 16:20:04 -0400
>> >>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> >>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> >>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >>>>> Message-ID: <4A5F8B74.6070404 at vt.edu>
>> >>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>> Hi Justin,
>> >>>>>> Thanks for the explanation of the difference between EM &
>> equilibration.
>> >>>>>> Since in my model, I: (i) only have the graphene sheet and ammonia
>> >>>>>> molecules spaced reasonably far apart from each other (1332 NH3
>> >>>>>> molecules in a 38x38x38 box) and from the graphene sheet (distance
>> >>>>>> between the closest ammonia molecule and the graphene sheet is
>> greater
>> >>>>>> than the molecular diameter of ammonia - maybe this is too close
>> and
>> >>>>>> could be causing my problem?); (ii) freeze the graphene sheet; I am
>> >>>>>> thinking equilibration is not required in my model. Please let
>> me know
>> >>>>>> if you think I still need to perform equilibration.
>> >>>>>>
>> >>>>>> Yes, the EM did converge satisfactorily. Here is the output from
>> EM:
>> >>>>>> Steepest Descents converged to Fmax < 250 in 61 steps
>> >>>>>> Potential Energy = 4.6094102e+04
>> >>>>>> Maximum force = 2.4543298e+02 on atom 1
>> >>>>>> Norm of force = 7.5803179e+03
>> >>>>>>
>> >>>>>> Is this a reasonable value for FMax?
>> >>>>>>
>> >>>>> Your Fmax looks fine. Why is it necessary to freeze the graphene
>> sheet? Why
>> >>>>> not use position restraints (to rule out funky behavior of being
>> frozen)?
>> >>>>>
>> >>>>> Did you ever obtain a trajectory with enough frames that you
>> could watch? What
>> >>>>> happened?
>> >>>>>
>> >>>>> -Justin
>> >>>>>
>> >>>>>> Thanks again for your help.
>> >>>>>>
>> >>>>>> Darrell
>> >>>>>>
>> >>>>>>
>> >>>>>>> Date: Thu, 16 Jul 2009 07:15:12 -0400
>> >>>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> >>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> >>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >>>>>>> Message-ID: <4A5F0BC0.4020200 at vt.edu>
>> >>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>>>> Hi Mark,
>> >>>>>>>> I do not do any equilibration, I only do energy minimization
>> as in the
>> >>>>>>>> "GROMACS Tutorial for Solvation Study of Spider Toxin
>> Peptide". Please
>> >>>>>>>> let me know if I need to do equilibration and what is the
>> difference
>> >>>>>>>> between energy minimization and equilibration as this is not
>> clear to me.
>> >>>>>>>>
>> >>>>>>> Did the EM converge satisfactorily? What was Fmax?
>> >>>>>>>
>> >>>>>>> Unlike EM, equilibration is an MD process; for a protein
>> system, one generally
>> >>>>>>> position-restrains the protein and allows the surrounding
>> solvent to optimize
>> >>>>>>> around the structure.
>> >>>>>>>
>> >>>>>>> -Justin
>> >>>>>>>
>> >>>>>>>> Here is an mdp file for a run that actually completed
>> successfully:
>> >>>>>>>> title =Graphene
>> >>>>>>>> ;warnings =10
>> >>>>>>>> cpp =cpp
>> >>>>>>>> ;define =-DPOSRES
>> >>>>>>>> constraints =none
>> >>>>>>>> integrator =md
>> >>>>>>>> dt =0.002 ; ps
>> >>>>>>>> nsteps =10000
>> >>>>>>>> nstcomm =100
>> >>>>>>>> nstxout =100
>> >>>>>>>> ;nstvout =1000
>> >>>>>>>> nstfout =0
>> >>>>>>>> nstlog =100
>> >>>>>>>> nstenergy =100
>> >>>>>>>> nstlist =100
>> >>>>>>>> ns_type =grid
>> >>>>>>>> rlist =2.0
>> >>>>>>>> coulombtype =PME
>> >>>>>>>> rcoulomb =2.0
>> >>>>>>>> vdwtype =cut-off
>> >>>>>>>> rvdw =5.0
>> >>>>>>>> fourierspacing =0.12
>> >>>>>>>> fourier_nx =0
>> >>>>>>>> fourier_ny =0
>> >>>>>>>> fourier_nz =0
>> >>>>>>>> pme_order =4
>> >>>>>>>> ewald_rtol =1e-5
>> >>>>>>>> optimize_fft =yes
>> >>>>>>>>
>> >>>>>>>> ; This section freezes graphene lattice
>> >>>>>>>> energygrps = Grph NH3
>> >>>>>>>> energygrp_excl = Grph Grph
>> >>>>>>>> freezegrps = Grph ; Freeze graphene lattice
>> >>>>>>>> freezedim = Y Y Y; in all directions
>> >>>>>>>>
>> >>>>>>>> Tcoupl =berendsen
>> >>>>>>>> tau_t =0.5 0.5
>> >>>>>>>> tc-grps =NH3 Grph
>> >>>>>>>> ref_t =300 300
>> >>>>>>>>
>> >>>>>>>> ;coupl = parrinello-rahman
>> >>>>>>>> ;tau_p = 1.5
>> >>>>>>>> ;compressibility = 1.3
>> >>>>>>>> ;ref_p = 0.061
>> >>>>>>>>
>> >>>>>>>> gen_vel = yes
>> >>>>>>>> gen_temp = 300.0
>> >>>>>>>> gen_seed = 173529
>> >>>>>>>>
>> >>>>>>>> And here is a copy of an mdp file for a run that did not complete
>> >>>>>>>> successfully:
>> >>>>>>>>
>> >>>>>>>> title =Graphene
>> >>>>>>>> ;warnings =10
>> >>>>>>>> cpp =cpp
>> >>>>>>>> ;define =-DPOSRES
>> >>>>>>>> constraints =none
>> >>>>>>>> integrator =md
>> >>>>>>>> dt =0.002 ; ps
>> >>>>>>>> nsteps =30000
>> >>>>>>>> nstcomm =500
>> >>>>>>>> nstxout =500
>> >>>>>>>> ;nstvout =1000
>> >>>>>>>> nstfout =0
>> >>>>>>>> nstlog =500
>> >>>>>>>> nstenergy =500
>> >>>>>>>> nstlist =500
>> >>>>>>>> ns_type =grid
>> >>>>>>>> rlist =2.0
>> >>>>>>>> coulombtype =PME
>> >>>>>>>> rcoulomb =2.0
>> >>>>>>>> vdwtype =cut-off
>> >>>>>>>> rvdw =5.0
>> >>>>>>>> fourierspacing =0.12
>> >>>>>>>> fourier_nx =0
>> >>>>>>>> fourier_ny =0
>> >>>>>>>> fourier_nz =0
>> >>>>>>>> pme_order =4
>> >>>>>>>> ewald_rtol =1e-5
>> >>>>>>>> optimize_fft =yes
>> >>>>>>>>
>> >>>>>>>> ; This section freezes graphene lattice
>> >>>>>>>> energygrps = Grph NH3
>> >>>>>>>> energygrp_excl = Grph Grph
>> >>>>>>>> freezegrps = Grph ; Freeze graphene lattice
>> >>>>>>>> freezedim = Y Y Y; in all directions
>> >>>>>>>>
>> >>>>>>>> Tcoupl =berendsen
>> >>>>>>>> tau_t =0.5 0.5
>> >>>>>>>> tc-grps =NH3 Grph
>> >>>>>>>> ref_t =300 300
>> >>>>>>>>
>> >>>>>>>> ;coupl = parrinello-rahman
>> >>>>>>>> ;tau_p = 1.5
>> >>>>>>>> ;compressibility = 1.3
>> >>>>>>>> ;ref_p = 0.061
>> >>>>>>>>
>> >>>>>>>> gen_vel = yes
>> >>>>>>>> gen_temp = 300.0
>> >>>>>>>> gen_seed = 173529
>> >>>>>>>>
>> >>>>>>>> Please let me know what you think might be the problem.
>> >>>>>>>>
>> >>>>>>>> Thanks
>> >>>>>>>>
>> >>>>>>>> Darrell
>> >>>>>>>>
>> >>>>>>>>> Date: Thu, 16 Jul 2009 09:47:49 +1000
>> >>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> >>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not mapped)
>> >>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >>>>>>>>> Message-ID: <4A5E6AA5.4040809 at anu.edu.au>
>> >>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >>>>>>>>>
>> >>>>>>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>>>>>> Hi Mark,
>> >>>>>>>>>> Yes, I know that the box dimensions are defined in the last
>> line of the
>> >>>>>>>>>> .gro file and I have defined these dimensions as 38 nm x 38
>> nm x 38 nm
>> >>>>>>>>>> in the .gro file.
>> >>>>>>>>> OK.
>> >>>>>>>>>
>> >>>>>>>>>> I looked through my .gro file to ensure none of the atoms
>> had coordinates
>> >>>>>>>>>> outside the 38x38x38 box. While I was reviewing the file I
>> did notice
>> >>>>>>>>>> that some coordinates had negative values, slightly
>> negative, but
>> >>>>>>>>>> negative none the less. Could this be causing the
>> segmentation fault
>> >>>>>>>>>> between time step 10,000 and time step 30,000? Why wouldn't the
>> >>>>>>>>>> negative coordinates cause a segmentation fault much earlier?
>> >>>>>>>>> The absolute value of the coordinates is irrelevant.
>> >>>>>>>>>
>> >>>>>>>>> Your choice of 2.0 for rcoulomb is likely suboptimal for PME.
>> Some
>> >>>>>>>>> smaller value is probably more efficient, but this will not
>> be the cause
>> >>>>>>>>> of your problem.
>> >>>>>>>>>
>> >>>>>>>>> What is your system preparation regime? (i.e. EM +
>> equilibration)
>> >>>>>>>>>
>> >>>>>>>>> Can you post a corrected and current .mdp file?
>> >>>>>>>>>
>> >>>>>>>>> Mark
>> >>>>>>>>>
>> >>>>>>>>>>> Date: Wed, 15 Jul 2009 16:59:21 +1000
>> >>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> >>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not
>> mapped)
>> >>>>>>>>>>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> >>>>>>>>>>> Message-ID: <4A5D7E49.9020700 at anu.edu.au>
>> >>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >>>>>>>>>>>
>> >>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>>>>>>>> Hi Justin,
>> >>>>>>>>>>>> I was experiencing the problem before someone suggested
>> using editconf so
>> >>>>>>>>>>>> I do not think the problem is being caused by editconf.
>> But anyway here
>> >>>>>>>>>>>> is my editconf command. Let me know if you a source of
>> error in this
>> >>>>>>>>>>>> command line.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> editconf -f graphene.gro -n index.ndx -o graphene_ec.gro
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> I did not want to add in additional space between the
>> solvent and the box
>> >>>>>>>>>>>> as I saw no reason for doing so. And hence that is why I
>> originally did
>> >>>>>>>>>>>> not use editconf.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> My box dimensions are 38nm x 38nm x 38nm.
>> >>>>>>>>>>> The box dimensions are defined in the bottom line of the
>> .gro file, and
>> >>>>>>>>>>> not by the positions of the atoms in that file. If you
>> haven't ever set
>> >>>>>>>>>>> them to be suitable for your coordinates with editconf,
>> then they might
>> >>>>>>>>>>> not be.
>> >>>>>>>>>>>
>> >>>>>>>>>>> Mark
>> >>>>>>>>>>>
>> >>>>>>>>>>> I used cutoffs of 2 nm & 5 nm
>> >>>>>>>>>>>> for my system so ensure the cutoff occured at a distance
>> where the
>> >>>>>>>>>>>> potentials were stabalized (not changing). I guess I could
>> use shorter
>> >>>>>>>>>>>> cutoffs such as 1.5 nm & 2 nm and this may decrease my
>> computation time.
>> >>>>>>>>>>>> I also thought that I needed to use larger cut-offs since
>> I am dealing
>> >>>>>>>>>>>> in the gas phase and there is greater ditance between the
>> atoms in my
>> >>>>>>>>>>>> simulation than in liquid-based simulations.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> In the .log files, I do not see any LINCS warnings or
>> neighborlist
>> >>>>>>>>>>>> errors.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> I ran gmxcheck on a .trr file and was presented with the
>> following
>> >>>>>>>>>>>> output:
>> >>>>>>>>>>>> *********************************************
>> >>>>>>>>>>>> Checking file mdtraj.trr
>> >>>>>>>>>>>> trn version: GMX_trn_file (single precision)
>> >>>>>>>>>>>> Reading frame 0 time 0.000
>> >>>>>>>>>>>> # Atoms 10482
>> >>>>>>>>>>>> Last frame 5 time 1.000
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Item #frames Timestep (ps)
>> >>>>>>>>>>>> Step 6 0.2
>> >>>>>>>>>>>> Time 6 0.2
>> >>>>>>>>>>>> Lambda 6 0.2
>> >>>>>>>>>>>> Coords 6 0.2
>> >>>>>>>>>>>> Velocities 6 0.2
>> >>>>>>>>>>>> Forces 0
>> >>>>>>>>>>>> Box 6 0.2
>> >>>>>>>>>>>> *********************************************
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> I ran two additional simulations with different values for
>> nsteps and
>> >>>>>>>>>>>> nstxxxx paramaters and have the following to report:
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> When I run a simulation with the following parameters it
>> completes
>> >>>>>>>>>>>> successfully and I see, in the log file, the system output
>> every 100
>> >>>>>>>>>>>> time steps.
>> >>>>>>>>>>>> nsteps =10000
>> >>>>>>>>>>>> nstcomm =100
>> >>>>>>>>>>>> nstxout =100
>> >>>>>>>>>>>> nstfout =0
>> >>>>>>>>>>>> nstlog =100
>> >>>>>>>>>>>> nstenergy =100
>> >>>>>>>>>>>> nstlist =100
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> When I run a simulation with the following parameters it
>> fails with a
>> >>>>>>>>>>>> sementation fault and, in the log file, I do not see
>> system output every
>> >>>>>>>>>>>> 500 time steps.
>> >>>>>>>>>>>> nsteps =30000
>> >>>>>>>>>>>> nstcomm =500
>> >>>>>>>>>>>> nstxout =500
>> >>>>>>>>>>>> nstfout =0
>> >>>>>>>>>>>> nstlog =500
>> >>>>>>>>>>>> nstenergy =500
>> >>>>>>>>>>>> nstlist =500
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Please let me know what you think might be the problem.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Thank you very much.
>> >>>>>>>>>>>>
>> >>>>>>>>>>>> Darrell
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>
>> >>>>>>>>>>>>> Date: Mon, 13 Jul 2009 15:37:15 -0400
>> >>>>>>>>>>>>> From: "Justin A. Lemkul" <jalemkul at vt.edu>
>> >>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address not
>> mapped)
>> >>>>>>>>>>>>> To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> >>>>>>>>>>>>> Message-ID: <4A5B8CEB.4020609 at vt.edu>
>> >>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>>>>>>>>>> Hi Mark,
>> >>>>>>>>>>>>>> I used editconf on my .gro file with zero space between
>> my solvent and
>> >>>>>>>>>>>>>> the box and the resulting box had the exact same
>> dimension as the
>> >>>>>>>>>>>>>> initial box. I also performed a number of simulation
>> runs with different
>> >>>>>>>>>>>>> If you're using editconf to define zero space, what's the
>> point? I only ask
>> >>>>>>>>>>>>> because it is a potential source of error if you think
>> you're adding zero space,
>> >>>>>>>>>>>>> but something else might be going on. Maybe you can post
>> your editconf command
>> >>>>>>>>>>>>> line.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> What are your box dimensions? Are cut-off lengths of 2.0
>> and 5.0 nm appropriate
>> >>>>>>>>>>>>> for your system? How did you determine that these
>> cut-off's should be used?
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>> mdp parameters hoping this would provide me some
>> indication of the cause
>> >>>>>>>>>>>>>> of the fault but to no avail. I looked through the log
>> files, error
>> >>>>>>>>>>>>>> files, and output files and could not find any output to
>> help me
>> >>>>>>>>>>>>>> identify the source of my error.
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>> It is very odd that Gromacs isn't report anything at all.
>> No LINCS warnings?
>> >>>>>>>>>>>>> No neighborlist errors? These would be in the .log file.
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>> Could you please let me know how I can look at my
>> structure at each point
>> >>>>>>>>>>>>>> as you indicate below as I do not see any files output
>> that provide me
>> >>>>>>>>>>>>>> to do so? I tried to look at the .trr file but when I
>> try to load it
>> >>>>>>>>>>>>>> into VMD, it causes an error. I am assuming this error
>> is caused because
>> >>>>>>>>>>>>>> the .trr file did not complete correctly due to the
>> segmentation fault.
>> >>>>>>>>>>>>>> Please advise.
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>> How early is the segmentation fault occurring? I have
>> found it useful sometimes
>> >>>>>>>>>>>>> to set nstxout (or nstxtcout) = 1 to try to catch the
>> first few frames if the
>> >>>>>>>>>>>>> explosion is occurring early. In any case, gmxcheck will
>> help determine how
>> >>>>>>>>>>>>> many frames are present, as well as the integrity of the
>> file (broken frames, etc).
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> -Justin
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>>> Thanks.
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>> Darrell
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>> Date: Tue, 07 Jul 2009 09:19:42 +1000
>> >>>>>>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> >>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address
>> not mapped)
>> >>>>>>>>>>>>>>> To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> >>>>>>>>>>>>>>> Message-ID: <4A52868E.6010807 at anu.edu.au>
>> >>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>> format=flowed
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>>>>>>>>>>>> Hi Mark,
>> >>>>>>>>>>>>>>>> I added the energy group exclusions as indicated in
>> your previous
>> >>>>>>>>>>>>>>>> response but am still experiencing the same problem. I
>> looked at the
>> >>>>>>>>>>>>>>>> .log files and see that in one log file it tells me
>> that my box is
>> >>>>>>>>>>>>>>>> exploding. However, I do not have many molecules in my
>> simulation and
>> >>>>>>>>>>>>>>>> therefore do not think that it is possible that my box
>> is exploding from
>> >>>>>>>>>>>>>>>> pressure.
>> >>>>>>>>>>>>>>> Sure, but if there's something malformed with your
>> model physics or
>> >>>>>>>>>>>>>>> starting configuration, then large forces can make
>> anything explode.
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>> Look at your structures at each point and see where
>> things start to go
>> >>>>>>>>>>>>>>> wrong. Make sure you've used editconf on your starting
>> structure to
>> >>>>>>>>>>>>>>> provide the right box dimensions.
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>> Mark
>> >>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>> Maybe if I re-state my simulation it will help you in
>> providing me
>> >>>>>>>>>>>>>>>> direction on what might be causing the problem. My
>> simulation consists
>> >>>>>>>>>>>>>>>> of a graphene lattice with a layer of ammonia
>> molecules above it. The
>> >>>>>>>>>>>>>>>> box is very large and there is lots of empty space in
>> the box. So I am a
>> >>>>>>>>>>>>>>>> little confused as to how the box could be exploding.
>> >>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>> Thanks again in advance for your help.
>> >>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>> Darrell Koskinen
>> >>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>> Date: Fri, 03 Jul 2009 11:41:45 +1000
>> >>>>>>>>>>>>>>>>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> >>>>>>>>>>>>>>>>> Subject: Re: [gmx-users] Segmentation Fault (Address
>> not mapped)
>> >>>>>>>>>>>>>>>>> To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> >>>>>>>>>>>>>>>>> Message-ID: <4A4D61D9.6080700 at anu.edu.au>
>> >>>>>>>>>>>>>>>>> Content-Type: text/plain; charset=ISO-8859-1;
>> format=flowed
>> >>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>> darrellk at ece.ubc.ca wrote:
>> >>>>>>>>>>>>>>>>>> Dear GROMACS Gurus,
>> >>>>>>>>>>>>>>>>>> I am experiencing a segmentation fault when mdrun
>> executes. My simulation
>> >>>>>>>>>>>>>>>>>> has a graphene lattice with an array (layer) of
>> ammonia molecules above
>> >>>>>>>>>>>>>>>>>> it. The box is three times the width of the graphene
>> lattice, three
>> >>>>>>>>>>>>>>>>>> times the length of the graphene lattice, and three
>> times the height
>> >>>>>>>>>>>>>>>>>> between the graphene lattice and the ammonia
>> molecules. I am including
>> >>>>>>>>>>>>>>>>>> the mdp file and the error message.
>> >>>>>>>>>>>>>>>>> Probably your system is exploding when integration
>> fails with excessive
>> >>>>>>>>>>>>>>>>> forces. You should look at the bottom of stdout,
>> stderr, *and* the .log
>> >>>>>>>>>>>>>>>>> file to diagnose. The error message you give below is
>> merely the
>> >>>>>>>>>>>>>>>>> diagnostic trace from the MPI library, and it not
>> useful for finding out
>> >>>>>>>>>>>>>>>>> what GROMACS thinks the problem might be. Further
>> advice below.
>> >>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>>
>> ***************************************************************************
>> >>>>>>>>>>>>>>>>>> .mdp file
>> >>>>>>>>>>>>>>>>>> title =FWS
>> >>>>>>>>>>>>>>>>>> ;warnings =10
>> >>>>>>>>>>>>>>>>>> cpp =cpp
>> >>>>>>>>>>>>>>>>>> ;define =-DPOSRES
>> >>>>>>>>>>>>>>>>>> ;constraints =all-bonds
>> >>>>>>>>>>>>>>>>>> integrator =md
>> >>>>>>>>>>>>>>>>>> dt =0.002 ; ps
>> >>>>>>>>>>>>>>>>>> nsteps =100000
>> >>>>>>>>>>>>>>>>>> nstcomm =1000
>> >>>>>>>>>>>>>>>>>> nstxout =1000
>> >>>>>>>>>>>>>>>>>> ;nstvout =1000
>> >>>>>>>>>>>>>>>>>> nstfout =0
>> >>>>>>>>>>>>>>>>>> nstlog =1000
>> >>>>>>>>>>>>>>>>>> nstenergy =1000
>> >>>>>>>>>>>>>>>>>> nstlist =1000
>> >>>>>>>>>>>>>>>>>> ns_type =grid
>> >>>>>>>>>>>>>>>>>> rlist =2.0
>> >>>>>>>>>>>>>>>>>> coulombtype =PME
>> >>>>>>>>>>>>>>>>>> rcoulomb =2.0
>> >>>>>>>>>>>>>>>>>> vdwtype =cut-off
>> >>>>>>>>>>>>>>>>>> rvdw =5.0
>> >>>>>>>>>>>>>>>>>> fourierspacing =0.12
>> >>>>>>>>>>>>>>>>>> fourier_nx =0
>> >>>>>>>>>>>>>>>>>> fourier_ny =0
>> >>>>>>>>>>>>>>>>>> fourier_nz =0
>> >>>>>>>>>>>>>>>>>> pme_order =4
>> >>>>>>>>>>>>>>>>>> ewald_rtol =1e-5
>> >>>>>>>>>>>>>>>>>> optimize_fft =yes
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> ; This section added in to freeze hydrogen atoms at
>> edge of graphene
>> >>>>>>>>>>>>>>>>>> lattice to prevent movement of lattice
>> >>>>>>>>>>>>>>>>>> ;energygrp_excl = Edge Edge Edge Grph Grph Grph
>> >>>>>>>>>>>>>>>>>> freezegrps = Edge Grph ; Hydrogen atoms in graphene
>> lattice are
>> >>>>>>>>>>>>>>>>>> associated with the residue Edge
>> >>>>>>>>>>>>>>>>> See comments in 7.3.24 of manual. You need the energy
>> group exclusions.
>> >>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>> Mark
>> >>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> freezedim = Y Y Y Y Y Y; Freeze hydrogen atoms in
>> all directions
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> ;Tcoupl =berendsen
>> >>>>>>>>>>>>>>>>>> ;tau_t =0.1 0.1
>> >>>>>>>>>>>>>>>>>> ;tc-grps =protein non-protein
>> >>>>>>>>>>>>>>>>>> ;ref_t = 300 300
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> ;Pcoupl = parrinello-rahman
>> >>>>>>>>>>>>>>>>>> ;tau_p = 0.5
>> >>>>>>>>>>>>>>>>>> ;compressibility = 4.5e-5
>> >>>>>>>>>>>>>>>>>> ;ref_p = 1.0
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> ;gen_vel = yes
>> >>>>>>>>>>>>>>>>>> ;gen_temp = 300.0
>> >>>>>>>>>>>>>>>>>> ;gen_seed = 173529
>> >>>>>>>>>>>>>>>>>>
>> ***************************************************************************
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>>
>> ***************************************************************************
>> >>>>>>>>>>>>>>>>>> ERROR IN OUTPUT FILE
>> >>>>>>>>>>>>>>>>>> [node16:25758] *** Process received signal ***
>> >>>>>>>>>>>>>>>>>> [node16:25758] Signal: Segmentation fault (11)
>> >>>>>>>>>>>>>>>>>> [node16:25758] Signal code: Address not mapped (1)
>> >>>>>>>>>>>>>>>>>> [node16:25758] Failing at address: 0xfffffffe1233e230
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 0] /lib64/libpthread.so.0
>> [0x3834a0de80]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 1]
>> /usr/lib64/libmd_mpi.so.4(pme_calc_pidx+0xd6)
>> >>>>>>>>>>>>>>>>>> [0x2ba295dd0606]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 2]
>> /usr/lib64/libmd_mpi.so.4(do_pme+0x808)
>> >>>>>>>>>>>>>>>>>> [0x2ba295dd4058]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 3]
>> /usr/lib64/libmd_mpi.so.4(force+0x8de)
>> >>>>>>>>>>>>>>>>>> [0x2ba295dba5be]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 4]
>> /usr/lib64/libmd_mpi.so.4(do_force+0x5ef)
>> >>>>>>>>>>>>>>>>>> [0x2ba295ddeaff]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 5] mdrun_mpi(do_md+0xe23) [0x411193]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 6] mdrun_mpi(mdrunner+0xd40)
>> [0x4142f0]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 7] mdrun_mpi(main+0x239) [0x4146f9]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 8]
>> /lib64/libc.so.6(__libc_start_main+0xf4)
>> >>>>>>>>>>>>>>>>>> [0x3833e1d8b4]
>> >>>>>>>>>>>>>>>>>> [node16:25758] [ 9] mdrun_mpi [0x40429a]
>> >>>>>>>>>>>>>>>>>> [node16:25758] *** End of error message ***
>> >>>>>>>>>>>>>>>>>> mpirun noticed that job rank 7 with PID 25758 on
>> node node16 exited on
>> >>>>>>>>>>>>>>>>>> signal 11 (Segmentation fault).
>> >>>>>>>>>>>>>>>>>> 7 processes killed (possibly by Open MPI)
>> >>>>>>>>>>>>>>>>>>
>> ***************************************************************************
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> Could you please let me know what you think may be
>> causing the fault?
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> Much thanks in advance.
>> >>>>>>>>>>>>>>>>>>
>> >>>>>>>>>>>>>>>>>> Darrell Koskinen
>> >>>>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>>>>>>>>> Please search the archive at
>> http://www.gromacs.org/search before posting!
>> >>>>>>>>>>>>>> Please don't post (un)subscribe requests to the list.
>> Use the
>> >>>>>>>>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>> >>>>>>>>>>>>>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>> >>>>>>>>>>>>>>
>> >>>>>>>>>>>>> --
>> >>>>>>>>>>>>> ========================================
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> Justin A. Lemkul
>> >>>>>>>>>>>>> Ph.D. Candidate
>> >>>>>>>>>>>>> ICTAS Doctoral Scholar
>> >>>>>>>>>>>>> Department of Biochemistry
>> >>>>>>>>>>>>> Virginia Tech
>> >>>>>>>>>>>>> Blacksburg, VA
>> >>>>>>>>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>> >>>>>>>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >>>>>>>>>>>>>
>> >>>>>>>>>>>>> ========================================
>> >>>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>>>>>>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> >>>>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>> >>>>>>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>> >>>>>>>>>>>> Can't post? Read
>> http://www.gromacs.org/mailing_lists/users.php
>> >>>>>>>>>>>>
>> >>>>>>>>>>> ------------------------------
>> >>>>>>>>>>>
>> >>>>>>>>>>> _______________________________________________
>> >>>>>>>>>>> gmx-users mailing list
>> >>>>>>>>>>> gmx-users at gromacs.org
>> >>>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>>>>>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> >>>>>>>>>>>
>> >>>>>>>>>>> End of gmx-users Digest, Vol 63, Issue 61
>> >>>>>>>>>>> *****************************************
>> >>>>>>>>>>>
>> >>>>>>>>>> _______________________________________________
>> >>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>>>>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> >>>>>>>>>> Please don't post (un)subscribe requests to the list. Use the
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>> >>>>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>>>>>>>>>
>> >>>>>>>> _______________________________________________
>> >>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> >>>>>>>> Please don't post (un)subscribe requests to the list. Use the
>> >>>>>>>> www interface or send it to gmx-users-request at gromacs.org.
>> >>>>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>>>>>>>
>> >>>>>>> --
>> >>>>>>> ========================================
>> >>>>>>>
>> >>>>>>> Justin A. Lemkul
>> >>>>>>> Ph.D. Candidate
>> >>>>>>> ICTAS Doctoral Scholar
>> >>>>>>> Department of Biochemistry
>> >>>>>>> Virginia Tech
>> >>>>>>> Blacksburg, VA
>> >>>>>>> jalemkul[at]vt.edu | (540) 231-9080
>> >>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >>>>>>>
>> >>>>>>> ========================================
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> ------------------------------
>> >>>>>>>
>> >>>>>>> _______________________________________________
>> >>>>>>> gmx-users mailing list
>> >>>>>>> gmx-users at gromacs.org
>> >>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> >>>>>>>
>> >>>>>>> End of gmx-users Digest, Vol 63, Issue 74
>> >>>>>>> *****************************************
>> >>>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>>> Please search the archive at http://www.gromacs.org/search
>> before posting!
>> >>>>>> Please don't post (un)subscribe requests to the list. Use the
>> >>>>>> www interface or send it to gmx-users-request at gromacs.org.
>> >>>>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>>>>>
>> >>>>> --
>> >>>>> ========================================
>> >>>>>
>> >>>>> Justin A. Lemkul
>> >>>>> Ph.D. Candidate
>> >>>>> ICTAS Doctoral Scholar
>> >>>>> Department of Biochemistry
>> >>>>> Virginia Tech
>> >>>>> Blacksburg, VA
>> >>>>> jalemkul[at]vt.edu | (540) 231-9080
>> >>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >>>>>
>> >>>>> ========================================
>> >>>>>
>> >>>>>
>> >>>>> ------------------------------
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> gmx-users mailing list
>> >>>>> gmx-users at gromacs.org
>> >>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> >>>>>
>> >>>>> End of gmx-users Digest, Vol 63, Issue 79
>> >>>>> *****************************************
>> >>>>>
>> >>>> _______________________________________________
>> >>>> gmx-users mailing list gmx-users at gromacs.org
>> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> >>>> Please don't post (un)subscribe requests to the list. Use the
>> >>>> www interface or send it to gmx-users-request at gromacs.org.
>> >>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>>>
>> >>> --
>> >>> ========================================
>> >>>
>> >>> Justin A. Lemkul
>> >>> Ph.D. Candidate
>> >>> ICTAS Doctoral Scholar
>> >>> Department of Biochemistry
>> >>> Virginia Tech
>> >>> Blacksburg, VA
>> >>> jalemkul[at]vt.edu | (540) 231-9080
>> >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >>>
>> >>> ========================================
>> >>>
>> >>>
>> >>> ------------------------------
>> >>>
>> >>> _______________________________________________
>> >>> gmx-users mailing list
>> >>> gmx-users at gromacs.org
>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> >>>
>> >>> End of gmx-users Digest, Vol 63, Issue 85
>> >>> *****************************************
>> >>>
>> >> _______________________________________________
>> >> gmx-users mailing list gmx-users at gromacs.org
>> >> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> >> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> >> Please don't post (un)subscribe requests to the list. Use the
>> >> www interface or send it to gmx-users-request at gromacs.org.
>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> >>
>> >
>> >--
>> >========================================
>> >
>> >Justin A. Lemkul
>> >Ph.D. Candidate
>> >ICTAS Doctoral Scholar
>> >Department of Biochemistry
>> >Virginia Tech
>> >Blacksburg, VA
>> >jalemkul[at]vt.edu | (540) 231-9080
>> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>
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