[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 12 19:36:16 CET 2011
Steve Vivian wrote:
> On 03/12/2011 12:51 PM, Justin A. Lemkul wrote:
> Getting hard to follow, so I put my new comments in blue.
> Output from Energy Minimization
>
> Steepest Descents converged to Fmax < 1000 in 1814 steps
> Potential Energy = -3.81270276926664e+05
> Maximum force = 9.38712770623942e+02 on atom 2292
> Norm of force = 2.88274347161761e+01
>
>
>
>>
>> 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
>>> #ifdef STRONG_POSRES
>>> #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.
>>
>> -Justin
> Put my comments in blue to make it easier to read.
>
> I apologize for the poor description here.
> The first loop begins with the System_inflate.gro file created in the
> earlier process. The rest of the first loop is shown.
>
> At the beginning of the second loop, the input file is
> system_shrink_1.gro, which was the output file at the end of loop 1.
> Proceed through the loop, updating the n from 1 to 2 in each step.
> Output file is system_shrink_2.gro.
>
> Input file for loop 3 is system_shrink_3.gro, ....
>
> ....Output from loop 26 is system_shrink_26.gro and output on screen
> provides information on updated Lipid area which has achieved target value.
>
> Then proceed to add water (after changing vdw radius of C atoms)
> Add ions
> EM again
> Then Equilibrate.
>
>
> Output from Energy Minimization (after addition of water and ions)
>
> Steepest Descents converged to Fmax < 1000 in 1814 steps
> Potential Energy = -3.81270276926664e+05
> Maximum force = 9.38712770623942e+02 on atom 2292
> Norm of force = 2.88274347161761e+01
>
>
This output indicates to me that the system is completely reasonable. If you
send me your .gro and .top (off-list), I will try to debug and report back if I
can find anything.
To confirm, you are using Gromacs 4.5.3? What version of FFTW? What hardware?
What compilers were used for the installation?
-Justin
>
>>
>>> 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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
More information about the gromacs.org_gmx-users
mailing list