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.
1. get rid of the steric clash in the starting structure
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
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:
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
em_steep_1.mdp
Description: Binary data
em_steep_2.mdp
Description: Binary data
pr.mdp
Description: Binary data
nvt.mdp
Description: Binary data
npt.mdp
Description: Binary data
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