Canavan Task 10 - Molecular Dynamics Simulations

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Revision as of 14:45, 4 July 2012 by Vorbergs (talk | contribs) (energies)

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)