[gmx-users] Segmentation Fault (Address not mapped)
darrellk at ece.ubc.ca
darrellk at ece.ubc.ca
Thu Jul 16 21:36:34 CEST 2009
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?
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
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>>>>>> 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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>>>>> *****************************************
>>>>>
>>>> _______________________________________________
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>
>--
>========================================
>
>Justin A. Lemkul
>Ph.D. Candidate
>ICTAS Doctoral Scholar
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
>
>------------------------------
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