Hi All,<br><br> 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.<br>
<br> 1. get rid of the steric clash in the starting structure<br> 2. after doing pdb2gmx, then minimze the protein<br> 3, use "-bt dodecahedron -d 0.9 -c" in the command line of editconf<br> 4, after doing genbox, first minimize the water with protein rigid and then minimize the whole system<br>
5, run md simulation with position restraint for protein heavy atoms with nose-hoover thermostat for 20ps<br> 6, run NPT simulations with nose-hoover thermostat and Parrinello-Rahman thermostat for 500ps<br> 7, run NVT simulation for another 100ps<br>
8, then energy minimze the whole system again.<br><br>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:<br>
<br><span style="color: rgb(153, 153, 255);"> <span style="color: rgb(102, 102, 102);"> Step Time Lambda Annealing</span></span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 180000 360.00003 0.00000 1.00000</span><br style="color: rgb(102, 102, 102);">
<br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Rel. Constraint Deviation: Max between atoms RMS</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Before LINCS 0.045887 47 48 0.004584</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> After LINCS 0.000020 752 755 0.000003</span><br style="color: rgb(102, 102, 102);"><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Energies (kJ/mol)</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 2.08335e+03 1.59908e+02 2.95659e+03 1.17109e+03 1.27711e+04</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 4.10779e+04 -1.37728e+03 -2.89916e+05 -5.82443e+04 -2.89318e+05</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> Kinetic En. Total Energy Temperature Pressure (bar)</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 5.25584e+04 -2.36759e+05 2.96920e+02 -1.07683e+02</span><br style="color: rgb(102, 102, 102);">
<br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Step Time Lambda Annealing</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 185000 370.00003 0.00000 1.00000</span><br style="color: rgb(102, 102, 102);">
<br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Rel. Constraint Deviation: Max between atoms RMS</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Before LINCS 0.052014 70 71 0.005149</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> After LINCS 0.000011 214 215 0.000002</span><br style="color: rgb(102, 102, 102);"><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> Energies (kJ/mol)</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> Angle Proper Dih. Ryckaert-Bell. LJ-14 Coulomb-14</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 2.33684e+03 1.42695e+02 2.91169e+03 1.18452e+03 1.28507e+04</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> LJ (SR) Disper. corr. Coulomb (SR) Coulomb (LR) Potential</span><br style="color: rgb(102, 102, 102);"><span style="color: rgb(102, 102, 102);"> 4.06987e+04 -1.37332e+03 -2.88889e+05 -5.83180e+04 -2.88455e+05</span><br style="color: rgb(102, 102, 102);">
<span style="color: rgb(102, 102, 102);"> Kinetic En. Total Energy Temperature</span><br><br>The *.mdp files are also attached. Any help will be highly appreciated. Thank you.<br><br><br>Best,<br>Lan<br>