[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault

Justin A. Lemkul jalemkul at vt.edu
Sat Mar 12 18:51:40 CET 2011

Steve Vivian wrote:
> Based on a preliminary test using multiple threads, the issue is not
> resolved.
> This leads me to believe that my Unit Cell is not built properly.
> Below is the procedure used to build the unit cell.  I have reviewed it many
> times, but I would appreciate any input regarding potential improvements,
> specifically on the line using trjconv in the EM/Shrink loop.
> Safe up to here, (I hope)...
> cat KALP_newbox.gro dppc128_whole.gro > system.gro
> update minim.mdp
> ; Strong position restraints for InflateGRO
> #include "strong_posre.itp"
> #endif
> Create Strong Position Restraint for protein
> genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> Scale Lipid positions by a factor of 4
> perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat
> Begin loop of repeated Energy Minimizations and Shrinking 
> (repeat loop approximately 25 times until area is approx 71 Ang sq)
> Begin LOOP (from n=1 to n = 26)
> 	grompp -f minim.mdp -c systm_inf_n.gro -p topol.top -o em_n.tpr
> 	mdrun -v -deffnm em_n
> 	trjconv -s em_n.tpr -f em_n.gro -o em_n_out.gro -pbc mol -ur compact
> 	perl inflategro.pl em_n_out.gro 0.95 DPPC 0 sys_shr_1.gro 5

One problem here: you start the loop every time with system_inf_n?  What is 
system_inf_n?  It seems that you should start one (non-loop) shrink and then 
process the subsequent shrinking steps from there.  At the end of the loop, you 
write to sys_shr_1.gro, which then never gets used again.


> ar_shr1.dat
> End LOOP
> Add water 
> Add ions
> Re-run EM
> Equilibrate (and watch it all explode)
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Justin A. Lemkul
> Sent: Thursday, March 10, 2011 12:56 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation
> Fault
> Steve Vivian wrote:
>> On 03/08/2011 10:23 PM, Justin A. Lemkul wrote:
>>> Steve Vivian wrote:
>>>> New to Gromacs.
>>>> Worked my way through the tutorial with relatively few issues until 
>>>> the Equilibration stage.  My system blows up!!
>>>> Returned to the Topology stage and rebuilt my system ensuring that I 
>>>> followed the procedure correctly for the InflateGro process.  It 
>>>> appears to be correct, reasonable lipid area, no water inside my 
>>>> bilayer, vmd shows a structure which appears normal (although I am 
>>>> new to this).  There are voids between bilayer and water molecules, 
>>>> but this is to be expected, correct?
>>>> Energy Minimization repeatedly produces results within the expected 
>>>> range.
>>>> Again system blows up at equilibration, step 0 segmentation fault.  
>>>> Regardless of whether I attempt the NVT or Anneal_Npt process (using 
>>>> the provided mdp files, including the updates for restraints on the 
>>>> protein and the lipid molecules).
>>>> I have attempted many variations of the nvt.mdp and anneal_npt.mdp 
>>>> files hoping to resolve my issue, but with no success.  I will post 
>>>> the log information from the nvt.mdp file included in the tutorial.
>>>> Started mdrun on node 0 Tue Mar  8 15:42:35 2011
>>>>            Step           Time         Lambda
>>>>               0        0.00000        0.00000
>>>> Grid: 9 x 9 x 9 cells
>>>>    Energies (kJ/mol)
>>>>        G96Angle            Proper Dih.      Improper Dih.          
>>>> LJ-14                 Coulomb-14
>>>>     8.52380e+01        6.88116e+01    2.23939e+01       
>>>> -3.03546e+01    2.71260e+03
>>>>         LJ (SR)              Disper. corr.           Coulomb (SR)   
>>>> Coul. recip.             Position Rest.
>>>>     1.49883e+04   -1.42684e+03       -2.78329e+05       
>>>> -1.58540e+05        2.57100e+00
>>>>       Potential            Kinetic En.               Total 
>>>> Energy                  Conserved En.               Temperature
>>>>    -4.20446e+05    *1.41436e+14        1.41436e+14        
>>>> 1.41436e+14            1.23343e+12*
>>>>  Pres. DC (bar)         Pressure (bar)       Constr. rmsd
>>>>    -1.56331e+02        5.05645e+12        1.18070e+01
>>>> As you can see the Potential Energy is reasonable, but the Kinetic 
>>>> Energy and Temperature seem unrealistic.
>>>> I am hoping that this is enough information for a more experienced 
>>>> Gromacs user to provide guidance. Note:  that I have tried all of the 
>>>> suggestions that I read on the mailing list and in the "blowing up" 
>>>> section of the manual, specifically:
>>>> -reduced time steps in Equilibration Stages
>>>> -reduced Fmax during EM stage (down as low as 100kJ which did not help)
>>>> -modified neighbours list parameters
>>>> Any help is appreciated. I can attach and forward any further 
>>>> information as required, please let me know.
>>> Which Gromacs version are you using?  It looks like you're running in 
>>> serial, is that correct?  Otherwise, please provide your mdrun command 
>>> line.  If you're using version 4.5.3 in serial, I have identified a 
>>> very problematic bug that seems to affect a wide variety of systems 
>>> that could be related:
>> Yes I am currently using Gromacs 4.5.3 in serial.
>>> http://redmine.gromacs.org/issues/715
>>> I have seen even the most robust tutorial systems fail as well, as 
>>> some new lab members experienced the same problem.  The workaround is 
>>> to run in parallel.
>> If I understand you correctly, the recommended workaround is to 
>> re-configure gromacs 4.5.3 with mpi enabled and complete the 
>> Equilibration and Production simulation in parallel.
> Strictly speaking, an external MPI library is no longer required.  Gromacs
> now 
> builds with internal threading support (as long as your hardware and
> compilers 
> support such features).  In fact, thread support builds by default if
> possible, 
> so if your mdrun has an -nt flag, you don't need to do anything else except
> use 
> "mdrun -nt (number of threads)" when running your command.
>> Do you have a recommendation for which mpi library to install (lam mpi 
>> seems to be referenced in other articles on the mailing list)?
> I've had good luck with OpenMPI in the past, but this is not strictly
> necessary 
> in all cases.
>> Are there documented installation procedures for this process (upgrading 
>> to gromacs with mpi enabled)?
> http://www.gromacs.org/Downloads/Installation_Instructions#Using_MPI
> -Justin
>> Thanks for your assistance.
>> Steve.
>>> -Justin
>>>> Regards,
>>>> Steve Vivian.
>>>> svivian at uwo.ca


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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