[gmx-users] confusion about segmentation fault during mdrun

Lan Hua lan.hua at gmail.com
Thu May 20 03:08:19 CEST 2010


Thanks.  The simulations are regular MD in explicit water at room
temperature.


Lan

On Wed, May 19, 2010 at 6:03 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Lan Hua wrote:
>
>> Hi Justin,
>>
>>   I appreciated your quick answers.  So if I understand correctly, using
>> constraints = hbonds with the time step of 2fs, it should be fine, right?
>>
>>
> Maybe.  If your goal is REMD (I'm not clear from your original post) then
> stability may be an issue at higher temperatures, in which case you may need
> to constrain all bonds or decrease your time step, maybe both.  At ambient
> temperatures, what you propose is likely stable.  Look into the relevant
> literature for similar force fields and applications to be sure.
>
> -Justin
>
>  Thanks,
>> Lan
>>
>>
>> On Wed, May 19, 2010 at 3:52 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Lan Hua wrote:
>>
>>        Hi Justin,
>>
>>          Thank you so much for your quick reply and good suggestions.
>>        The following is my answer.
>>
>>        On Wed, May 19, 2010 at 12:50 PM, Justin A. Lemkul
>>        <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>        <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>>           Lan Hua wrote:
>>
>>               Hi All,
>>
>>                    I understand that the error of segmentation fault
>>        may come
>>               from many reasons, but I just couldn't figure out the
>>        reason of
>>               this error in my simulations.  I want to run md
>>        simulations with
>>               explicit water for 20 structures of one domain (residue
>>        77-148)
>>               of calmodulin (PDB 1CFC).  These 20 starting structures
>>        are from
>>               one REMD simulation in implicit water.  The following is
>>        what I
>>               did to run simulations for these 20 structures.  I used
>>        gromacs
>>               version 3.1.4 with ffamber ports.  The force field is
>> amber03
>>               and water model is TIP3P.
>>
>>
>>           Do you have any particular reason for using software that is
>>        eight
>>           years old? You will get a massive performance upgrade with
>>        4.0.7, as
>>           well as the ability to use multiple processors per replica.  In
>>           versions prior to 4.0, you can only use one processor per
>>        REMD replica.
>>
>>        The reason that I am using gromacs 3.1.4 is to prepare some
>>        input files for simulations at folding at home in which version
>>        3.1.4 is recommended.
>>
>>
>>    OK, as long as you've got a reason...
>>
>>
>>
>>
>>                 1.  get rid of the steric clash in the starting structure
>>
>>
>>           What do you mean?  Energy minimization?  How did you did do this
>>           prior to step 2 (generating a topology)?
>>
>>        I used the "protein preparation wizard" which is implemented in
>>        maestro package to do this.   Actually in this wizard, energy
>>        minimization is performed on protein.
>>
>>                 2.  after doing pdb2gmx, then minimze the protein
>>                 3,   use "-bt dodecahedron -d 0.9 -c"  in the command
>>        line of
>>               editconf
>>                 4,  after doing genbox, first minimize the water with
>>        protein
>>               rigid and then minimize the whole system
>>
>>
>>           A lot of these steps are redundant and probably unnecessary.
>>         Some tips:
>>
>>
>> http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
>>
>>
>>        Thanks for the tips. I went to the link, but I am still a little
>>        bit confused about which steps are unnecessary.  You mean step 7
>>        and step 8?  I did this in case simulations at F at H would be
>> crashed.
>>
>>
>>    I just mean the repeated, separate energy minimizations.  I guess
>>    there's no harm in it, but generally I find that minimizing the
>>    protein in vacuo, then with and without restraints in solvent, etc.
>>    is unnecessary.  I'd suggest just building the system (solvent and
>>    all), and minimizing the whole thing (without restraints).  I don't
>>    think you stand to gain anything with your procedure.
>>
>>
>>
>>
>>                 5,  run md simulation with position restraint for protein
>>               heavy atoms with nose-hoover thermostat for 20ps
>>                 6,  run NPT simulations with nose-hoover thermostat and
>>               Parrinello-Rahman thermostat for 500ps
>>                 7,  run NVT simulation for another 100ps
>>                 8, then energy minimze the whole system again.
>>
>>               Every time, there are always "segmentation fault" in step
>>        6 for
>>               some starting structures which could be different in
>>        every try.
>>                I checked the energy, volume, pressure, temperature, etc
>> for
>>               the trajectories which are crashed because of segmentation
>>               fault,  but nothing was wrong.  I roughly checked the
>>        trajectory
>>               which looks fine.  I also couldn't find any useful
>>        information
>>               from the log file, which looks like the following:
>>
>>
>>           Using weak coupling (i.e. Berendsen) coupling is generally
>>           recommended for initial equilibration.  If a system is far from
>>           equilibrium (as it likely will be after adding patterned
>>        blocks of
>>           water with genbox), the N-H thermostat can allow for wild
>>        changes in
>>           the temperature of the system, leading to a collapse.
>>
>>           Your temperature coupling groups are also inappropriate:
>>
>>           Tcoupl                   = nose-hoover
>>           tc_grps                  = Protein  SOL  Na
>>           tau_t                    = 0.1      0.1     0.1
>>
>>           Never couple solvent and ions separately; it can lead to
>>        instability:
>>
>>           http://www.gromacs.org/Documentation/Terminology/Thermostats
>>
>>
>>        These are good suggestions.  Thanks.  So use Berendsen coupling
>>        for both temperature and pressure coupling for initial
>>        equilibration, for example position restrained NVT followed by
>>        NPT, right? I have another
>>
>>
>>    At least for the thermostat, but yes, probably it can't hurt to use
>>    weak coupling for both temperature and pressure.
>>
>>
>>        question.  If I choose constraints = hbonds instead of
>>        constraints = all-bonds in NPT simulation, what will happen?
>>
>>
>>    You constrain heavy atom-H bonds instead of all bonds.  Using fewer
>>    constraints may or may not affect the magnitude of the time step you
>>    can use, but generally X-H bonds are the highest frequency and thus
>>    are the least stable with long time steps.
>>
>>    -Justin
>>
>>
>>        Best,
>>
>>        Lan
>>
>>           -Justin
>>
>>
>>                         Step           Time         Lambda      Annealing
>>                       180000      360.00003        0.00000        1.00000
>>
>>                 Rel. Constraint Deviation:  Max    between atoms     RMS
>>                     Before LINCS         0.045887     47     48   0.004584
>>                      After LINCS         0.000020    752    755   0.000003
>>
>>                 Energies (kJ/mol)
>>                        Angle    Proper Dih. Ryckaert-Bell.
>> LJ-14            Coulomb-14
>>                  2.08335e+03    1.59908e+02    2.95659e+03
>> 1.17109e+03           1.27711e+04
>>                      LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb
>>        (LR)             Potential
>>                  4.10779e+04   -1.37728e+03   -2.89916e+05
>>  -5.82443e+04          -2.89318e+05
>>                  Kinetic En.   Total Energy    Temperature Pressure (bar)
>>                  5.25584e+04   -2.36759e+05    2.96920e+02   -1.07683e+02
>>
>>                         Step           Time         Lambda      Annealing
>>                       185000      370.00003        0.00000        1.00000
>>
>>                 Rel. Constraint Deviation:  Max    between atoms     RMS
>>                     Before LINCS         0.052014     70     71   0.005149
>>                      After LINCS         0.000011    214    215   0.000002
>>
>>                 Energies (kJ/mol)
>>                        Angle    Proper Dih. Ryckaert-Bell.
>> LJ-14            Coulomb-14
>>                  2.33684e+03    1.42695e+02    2.91169e+03
>> 1.18452e+03           1.28507e+04
>>                      LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb
>>        (LR)             Potential
>>                  4.06987e+04   -1.37332e+03   -2.88889e+05
>>  -5.83180e+04          -2.88455e+05
>>                  Kinetic En.   Total Energy    Temperature
>>
>>               The *.mdp files are also attached.   Any help will be highly
>>               appreciated.  Thank you.
>>
>>
>>               Best,
>>               Lan
>>
>>
>>           --     ========================================
>>
>>           Justin A. Lemkul
>>           Ph.D. Candidate
>>           ICTAS Doctoral Scholar
>>           MILES-IGERT Trainee
>>           Department of Biochemistry
>>           Virginia Tech
>>           Blacksburg, VA
>>           jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
>>
>>        231-9080
>>
>>           http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
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>>
>>    --     ========================================
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>    ========================================
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>>
> --
> ========================================
>
> 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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