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
--
========================================
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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