[gmx-users] confusion about segmentation fault during mdrun
Lan Hua
lan.hua at gmail.com
Thu May 20 00:45:02 CEST 2010
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> 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.
>
> 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.
>
> 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 question. If
I choose constraints = hbonds instead of constraints = all-bonds in NPT
simulation, what will happen?
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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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