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

Steve Vivian svivian at uwo.ca
Sat Mar 12 18:05:30 CET 2011

Based on a preliminary test using multiple threads, the issue is not
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"

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

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

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
builds with internal threading support (as long as your hardware and
support such features).  In fact, thread support builds by default if
so if your mdrun has an -nt flag, you don't need to do anything else except
"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
in all cases.

> Are there documented installation procedures for this process (upgrading 
> to gromacs with mpi enabled)?



> 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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