Difference between revisions of "Canavan Task 10 - Molecular Dynamics Simulations"
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Total Energy -485680 54 886.726 -252.262 (kJ/mol) |
Total Energy -485680 54 886.726 -252.262 (kJ/mol) |
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+ | ===distances between periodic boundaries=== |
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+ | The shortest periodic distance is 1.6456 (nm) at time 7675 (ps), |
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+ | between atoms 15 and 4507 |
Revision as of 17:51, 4 July 2012
Contents
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
reference temperature from _md.mdp: 298K (thermostat:v-rescale)
Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Temperature 297.914 0.0072 1.38693 -0.00042403 (K)
Pressure:
reference pressure from _md.mdp: 1.0 (Berendsen barostat)
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)
distances between periodic boundaries
The shortest periodic distance is 1.6456 (nm) at time 7675 (ps), between atoms 15 and 4507