[gmx-users] Fwd: KALP-15 in DPPC Tutorial Step 0 Segmentation Fault
Steve Vivian
svivian at uwo.ca
Sat Mar 12 19:32:20 CET 2011
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
>
>> 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
>>>>>
>>>>>
>>>>>
>>
>
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