[gmx-users] confusion about segmentation fault during mdrun

[Justin A. Lemkul]

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.

>    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)?

>    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

>    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

-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
> 

-- 
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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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