Canavan Task 10 - Molecular Dynamics Simulations
Protocol
Further information can be found in the protocol.
Wildtype 2O4H
The commands can be found in the protocol.
gmxcheck
There are 2000 time frames, with a resolution of 5 psec. Therefore the whole simulation ran for 10000 psec = 10 nsec.
There are several atoms outside of the box.
atom# name residue r_vdw coordinate 406 HE1 HIS 23 0.04 5.3 8.72 2.92 408 HE2 HIS 23 0.04 5.47 8.69 2.73 480 HB1 ASN 27 0.04 5.14 8.67 2.39 482 CG ASN 27 0.15 5.32 8.7 2.29 483 OD1 ASN 27 0.105 5.32 8.7 2.17 484 ND2 ASN 27 0.11 5.41 8.79 2.35 485 HD21 ASN 27 0.04 5.41 8.79 2.45 486 HD22 ASN 27 0.04 5.47 8.84 2.29 500 MCB1 ALA 29 0 5.68 8.69 1.97 501 MCB2 ALA 29 0 5.63 8.68 2.05
log file
energies
Convergence of energies can be observed.
Temperature Energy Average Err.Est. RMSD Tot-Drift
Temperature 297.914 0.0072 1.38693 -0.00042403 (K)
Pressure:
Energy Average Err.Est. RMSD Tot-Drift
Pressure 1.00763 0.018 111.943 -0.0713928 (bar)
Potential:
Energy Average Err.Est. RMSD Tot-Drift
Potential -592161 55 721.947 -252.112 (kJ/mol)
Total energy:
Energy Average Err.Est. RMSD Tot-Drift
Total Energy -485680 54 886.726 -252.262 (kJ/mol)