[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 12 20:10:26 CET 2011
Steve Vivian wrote:
> On 03/12/2011 01:36 PM, Justin A. Lemkul wrote:
>>
>>
>> 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
>
>
> Using Gromacs 4.5.3 and FFTW 3.2.2 both compiled for double precision.
> It has been a while since I compiled so I'm not exactly sure, but I
> recall updating gcc and gfortran during the process.
> Hardware, what type of specifics are you looking for? # of processors
> and speed?
> Attached are current Energy Minimized file and topology file.
>
Hardware and compiler specs are unnecessary. The problem is the coordinate file
itself. Look at it in your favorite visualization program and you will see that
the lipid headgroups are completely collapsed in on one another. I don't know
how or why this happened. If you're using the DPPC topology from Tieleman and
the .mdp files given in the tutorial, I see no reason for this totally unstable
configuration. I have never used double precision (and it is not necessary for
standard MD, and only serves to slow your runs down), so it would be interesting
to see if the problem is a result of double vs. single precision. I can
successfully re-minimize the coordinate file you sent me using single precision:
Steepest Descents converged to Fmax < 1000 in 335 steps
Potential Energy = -6.3605750e+04
Maximum force = 7.1865680e+02 on atom 115
Norm of force = 3.9649860e+01
For now, I would suggest you test the precision issue. Install Gromacs again
(making note of your compiler versions, because this is important to know!) in
single precision and try to re-minimize the system and proceed. No need to
completely re-build it, as you should be able to just run a new EM on your
existing system like I did.
-Justin
> Steve.
>
>
>>
>>>
>>>>
>>>>> 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
========================================
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